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Yu S, Sahito ZA, Lu M, Huang Q, Du P, Chen D, Lian J, Feng Y, He Z, Yang X. Soil water stress alters differentially relative metabolic pathways affecting growth performance and metal uptake efficiency in a cadmium hyperaccumulator ecotype of Sedum alfredii. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:88986-88997. [PMID: 37450188 DOI: 10.1007/s11356-023-28691-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023]
Abstract
Modeling plants for biomass production and metal uptake from surrounding environment is strongly dependent on the moisture content of soil. Therefore, experiments were conducted to find out how soil moisture affects the phenotypic traits, photosynthetic efficiency, metabolic profile, and metal accumulation in the hyperaccumulating ecotype of Sedum alfredii (S. alfredii). A total of six water potential gradients were set: 0 ~ -15 kPa (T1), -15 ~ -30 kPa (T2), -30 ~ -45 kPa (T3), -45 ~ -60 kPa (T4), -60 ~ -75 kPa (T5), and -75 ~ -90 kPa (T6). Different water potential treatments had a significant effect on plant growth and metal uptake efficiency. Compared to T3, T2 was more effective in promoting plant growth and development, with an increase in biomass of 23% and 17% in both fresh weight (FW) and dry weight (DW), respectively. T2 and T3 had the highest cadmium (Cd) content in the shoot (280.2 mg/kg) and (283.3 mg/kg), respectively, whereas T1 had the lowest values (204.7 mg/kg). Cd availability for plants in the soil was affected by moving soil moisture cycles. Changes in soil moisture that were either too high or too low compared to the ideal soil water content for S. alfredii growth resulted in a significant reduction in Cd accumulation in shoots. Tryptophan, phenylalanine, and other amino acids were accumulated in T5, whereas only tryptophan and phenylalanine slightly increased in T1. Sugars and alcohols such as sucrose, trehalose, mannitol, galactinol, and mannobiose increased in T5, while they decreased significantly in T1. Interestingly, in contrast to T1, the two impaired metabolic pathways in T5 (galactose and starch metabolism) were identified to be glucose metabolic pathways. These findings provide scientific information (based on experiments) to improve biomass production and metal uptake efficiency in hyperaccumulating ecotype of S. alfredii for phytoremediation-contaminated agricultural fields.
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Affiliation(s)
- Song Yu
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Zulfiqar Ali Sahito
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Min Lu
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Qiwei Huang
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Pengtao Du
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Dan Chen
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Jiapan Lian
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Ying Feng
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Zhenli He
- Institute of Food and Agricultural Sciences, Department of Soil and Water Sciences, Indian River Research and Education Center, University of Florida, Fort Pierce, FL, 34945, USA
| | - Xiaoe Yang
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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Ren Z, Qin L, Chen L, Xu H, Liu H, Guo H, Li J, Yang C, Hu H, Wu R, Zhou Y, Xue K, Liu B, Wang X. Spatial Lipidomics of EPSPS and PAT Transgenic and Non-Transgenic Soybean Seeds Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37318082 DOI: 10.1021/acs.jafc.3c01377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Herbicide-resistant soybeans are among the most widely planted transgenic crops. The in situ evaluation of spatial lipidomics in transgenic and non-transgenic soybeans is important for directly assessing the unintended effects of exogenous gene introduction. In this study, matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI)-based non-targeted analytical strategies were used for the first time for in situ detection and imaging of endogenous lipid distributions in transgenic (EPSPS and PAT genes) herbicide-resistant soybean (Glycine max Merrill) (S4003.14) and non-transgenic soybean (JACK) seeds. Statistical analysis revealed significant differences in lipids between S4003.14 and JACK seeds. The variable importance of projection analysis further revealed that 18 identified lipids, including six phosphatidylcholines (PCs), four phosphatidylethanolamines (PEs), five triacylglycerols (TAGs), and three cytidine diphosphate-diacylglycerols (CDP-DAGs), had the strongest differential expression between S4003.14 and JACK seeds. Among those, the upregulated expressions of PC(P-36:1), PC(36:2), PC(P-36:0), PC(37:5), PE(40:2), TAG(52:1), TAG(55:5), and CDP-DAG(37:2) and the downregulated expressions of PC (36:1), TAG(43:0), and three PEs (i.e., PE(P-38:1), PE(P-38:0), and PE(P-40:3)) were successfully found in the S4003.14 seeds, compared to these lipids detected in the JACK seeds. Meanwhile, the lipids of PC (44:8), CDP-DAG(38:0), and CDP-DAG(42:0) were uniquely detected in the S4003.14 soybean seeds, and TAG(45:2) and TAG(57:10) were detected as the unique lipids in the JACK seeds. The heterogeneous distribution of these lipids in the soybean seeds was also clearly visualized using MALDI-MSI. MSI results showed that lipid expression was significantly up/downregulated in S4003.14 seeds, compared to that in JACK seeds. This study improves our understanding of the unintended effects of herbicide-resistant EPSPS and PAT gene transfers on spatial lipidomes in soybean seeds and enables the continued progression of MALDI-MSI as an emerging, reliable, and rapid molecular imaging tool for evaluating unintended effects in transgenic plants.
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Affiliation(s)
- Zhentao Ren
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Liang Qin
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Lulu Chen
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Hualei Xu
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Haiqiang Liu
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Hua Guo
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Jinrong Li
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Chenyu Yang
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Hao Hu
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Ran Wu
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Yijun Zhou
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Kun Xue
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Biao Liu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Xiaodong Wang
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
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Liang M, Zhang X, Dong Q, Li H, Guo S, Luan H, Jia P, Yang M, Qi G. Metabolomics and Transcriptomics Provide Insights into Lipid Biosynthesis in the Embryos of Walnut ( Juglans regia L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:538. [PMID: 36771622 PMCID: PMC9921657 DOI: 10.3390/plants12030538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/31/2022] [Accepted: 01/05/2023] [Indexed: 06/18/2023]
Abstract
Walnut (Juglans regia L.) is an important woody oilseed tree species due to its commercial value. However, the regulation mechanism of walnut oil accumulation is still poorly understood, which restricted the breeding and genetic improvement of high-quality oil-bearing walnuts. In order to explore the metabolic mechanism that regulates the synthesis of walnut oil, we used transcriptome sequencing technology and metabolome technology to comprehensively analyze the key genes and metabolites involved in oil synthesis of the walnut embryo at 60, 90, and 120 days after pollination (DAP). The results showed that the oil and protein contents increased gradually during fruit development, comprising 69.61% and 18.32% of the fruit, respectively, during ripening. Conversely, the contents of soluble sugar and starch decreased gradually during fruit development, comprising 2.14% and 0.84%, respectively, during ripening. Transcriptome sequencing generated 40,631 unigenes across 9 cDNA libraries. We identified 51 and 25 candidate unigenes related to the biosynthesis of fatty acid and the biosynthesis of triacylglycerol (TAG), respectively. The expression levels of the genes encoding Acetyl-CoA carboxylase (ACCase), long-chain acyl-CoA synthetases (LACS), 3-oxoacyl-ACP synthase II (KASII), and glycerol-3-phosphate acyl transfer (GPAT) were upregulated at 60 DAP relative to the levels at 90 and 120 DAP, while the stearoyl-ACP-desaturase (SAD) and fatty acid desaturase 2 (FAD2) genes were highly abundantly expressed during all walnut developmental periods. We found that ABSCISIC ACID INSENSEITIVE3 (ABI3), WRINKLEDl (WRI1), LEAFY COTYLEDON1 (LEC1), and FUSCA3 (FUS3) may be key transcription factors involved in lipid synthesis. Additionally, the metabolomics analysis detected 706 metabolites derived from 18 samples, among which, 4 are implicated in the TAG synthesis, 2 in the glycolysis pathway, and 5 in the tricarboxylic acid cycle (TCA cycle) pathway. The combined analysis of the related genes and metabolites in TAG synthesis showed that phospholipid:diacylglycerol acyltransferase (PDAT) genes were highly abundantly expressed across walnut fruit developmental periods, and their downstream metabolite TAG gradually accumulated with the progression of fruit development. The FAD2 gene showed consistently higher expression during fruit development, and its downstream metabolites 18:2-PC and 18:3-PC gradually accumulated. The ACCase, LACS, SAD, FAD2, and PDAT genes may be crucial genes required for walnut oil synthesis. Our data will enrich public databases and provide new insights into functional genes related to lipid metabolism in walnut.
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Affiliation(s)
- Manman Liang
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
| | - Xuemei Zhang
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
- Technology Innovation Center of Hebei Province, Xingtai 054000, China
- Institute of Walnut Industry Technology of Hebei Province (Xingtai), Lincheng 054300, China
| | - Qinglong Dong
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
- Technology Innovation Center of Hebei Province, Xingtai 054000, China
- Institute of Walnut Industry Technology of Hebei Province (Xingtai), Lincheng 054300, China
| | - Han Li
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
- Technology Innovation Center of Hebei Province, Xingtai 054000, China
- Institute of Walnut Industry Technology of Hebei Province (Xingtai), Lincheng 054300, China
| | - Suping Guo
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
- Technology Innovation Center of Hebei Province, Xingtai 054000, China
- Institute of Walnut Industry Technology of Hebei Province (Xingtai), Lincheng 054300, China
| | - Haoan Luan
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
- Technology Innovation Center of Hebei Province, Xingtai 054000, China
- Institute of Walnut Industry Technology of Hebei Province (Xingtai), Lincheng 054300, China
| | - Peng Jia
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
- Technology Innovation Center of Hebei Province, Xingtai 054000, China
- Institute of Walnut Industry Technology of Hebei Province (Xingtai), Lincheng 054300, China
| | - Minsheng Yang
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
| | - Guohui Qi
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
- Technology Innovation Center of Hebei Province, Xingtai 054000, China
- Institute of Walnut Industry Technology of Hebei Province (Xingtai), Lincheng 054300, China
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Liu W, Meng L, Zhao W, Wang Z, Miao C, Wan Y, Jin W. Proteomic and Metabolomic Evaluation of Insect- and Herbicide-Resistant Maize Seeds. Metabolites 2022; 12:1078. [PMID: 36355161 PMCID: PMC9696663 DOI: 10.3390/metabo12111078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/27/2022] [Accepted: 11/02/2022] [Indexed: 05/27/2024] Open
Abstract
Label-free quantitative proteomic (LFQ) and widely targeted metabolomic analyses were applied in the safety evaluation of three genetically modified (GM) maize varieties, BBL, BFL-1, and BFL-2, in addition to their corresponding non-GM parent maize. A total of 76, 40, and 25 differentially expressed proteins (DEPs) were screened out in BBL, BFL-1, and BFL-2, respectively, and their abundance compared was with that in their non-GM parents. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that most of the DEPs participate in biosynthesis of secondary metabolites, biosynthesis of amino acids, and metabolic pathways. Metabolomic analyses revealed 145, 178, and 88 differentially accumulated metabolites (DAMs) in the BBL/ZH58, BFL-1/ZH58, and BFL-2/ZH58×CH72 comparisons, respectively. KEGG pathway enrichment analysis showed that most of the DAMs are involved in biosynthesis of amino acids, and in arginine and proline metabolism. Three co-DEPs and 11 co-DAMs were identified in the seeds of these GM maize lines. The proteomic profiling of seeds showed that the GM maize varieties were not dramatically different from their non-GM control. Similarly, the metabolomic profiling of seeds showed no dramatic changes in the GM/non-GM maize varieties compared with the GM/GM and non-GM/non-GM maize varieties. The genetic background of the transgenic maize was found to have some influence on its proteomic and metabolomic profiles.
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Affiliation(s)
| | | | | | | | | | | | - Wujun Jin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Zhang W, Wang Y, Zhang T, Zhang J, Shen L, Zhang B, Ding C, Su X. Transcriptomic Analysis of Mature Transgenic Poplar Expressing the Transcription Factor JERF36 Gene in Two Different Environments. Front Bioeng Biotechnol 2022; 10:929681. [PMID: 35774064 PMCID: PMC9237257 DOI: 10.3389/fbioe.2022.929681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
During the last several decades, a number of transgenic or genetically modified tree varieties with enhanced characteristics and new traits have been produced. These trees have become associated with generally unsubstantiated concerns over health and environmental safety. We conducted transcriptome sequencing of transgenic Populus alba × P. berolinensis expressing the transcription factor JERF36 gene (ABJ01) and the non-transgenic progenitor line (9#) to compare the transcriptional changes in the apical buds. We found that 0.77% and 1.31% of the total expressed genes were significant differentially expressed in ABJ01 at the Daqing and Qiqihar sites, respectively. Among them, 30%–50% of the DEGs contained cis-elements recognized by JERF36. Approximately 5% of the total number of expressed genes showed significant differential expression between Daqing and Qiqihar in both ABJ01 and 9#. 10 DEGs resulting from foreign gene introduction, 394 DEGs that resulted solely from the environmental differences, and 47 DEGs that resulted from the combination of foreign gene introduction and the environment were identified. The number of DEGs resulting from environmental factors was significantly greater than that resulting from foreign gene introduction, and the combined effect of the environmental effects with foreign gene introduction was significantly greater than resulting from the introduction of JERF36 alone. GO and KEGG annotation showed that the DEGs mainly participate in the photosynthesis, oxidative phosphorylation, plant hormone signaling, ribosome, endocytosis, and plant-pathogen interaction pathways, which play important roles in the responses to biotic and abiotic stresses ins plant. To enhance its adaptability to salt-alkali stress, the transgenic poplar line may regulate the expression of genes that participate in the photosynthesis, oxidative phosphorylation, MAPK, and plant hormone signaling pathways. The crosstalk between biotic and abiotic stress responses by plant hormones may improve the ability of both transgenic and non-transgenic poplars to defend against pathogens. The results of our study provide a basis for further studies on the molecular mechanisms behind improved stress resistance and the unexpected effects of transgenic gene expression in poplars, which will be significant for improving the biosafety evaluation of transgenic trees and accelerating the breeding of new varieties of forest trees resistant to environmental stresses.
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Affiliation(s)
- Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
| | - Yanbo Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
- Nanchang Institute of Technology, Nanchang, China
| | - Tengqian Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
| | - Jing Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
| | - Le Shen
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
| | - Bingyu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
- *Correspondence: Changjun Ding, ; Xiaohua Su,
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- *Correspondence: Changjun Ding, ; Xiaohua Su,
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Exploitation of Plant Growth Promoting Bacteria for Sustainable Agriculture: Hierarchical Approach to Link Laboratory and Field Experiments. Microorganisms 2022; 10:microorganisms10050865. [PMID: 35630310 PMCID: PMC9144938 DOI: 10.3390/microorganisms10050865] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 11/24/2022] Open
Abstract
To feed a world population, which will reach 9.7 billion in 2050, agricultural production will have to increase by 35–56%. Therefore, more food is urgently needed. Yield improvements for any given crop would require adequate fertilizer, water, and plant protection from pests and disease, but their further abuse will be economically disadvantageous and will have a negative impact on the environment. Using even more agricultural inputs is simply not possible, and the availability of arable land will be increasingly reduced due to climate changes. To improve agricultural production without further consumption of natural resources, farmers have a powerful ally: the beneficial microorganisms inhabiting the rhizosphere. However, to fully exploit the benefits of these microorganisms and therefore to widely market microbial-based products, there are still gaps that need to be filled, and here we will describe some critical issues that should be better addressed.
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Ashraf MF, Hou D, Hussain Q, Imran M, Pei J, Ali M, Shehzad A, Anwar M, Noman A, Waseem M, Lin X. Entailing the Next-Generation Sequencing and Metabolome for Sustainable Agriculture by Improving Plant Tolerance. Int J Mol Sci 2022; 23:651. [PMID: 35054836 PMCID: PMC8775971 DOI: 10.3390/ijms23020651] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 02/07/2023] Open
Abstract
Crop production is a serious challenge to provide food for the 10 billion individuals forecasted to live across the globe in 2050. The scientists' emphasize establishing an equilibrium among diversity and quality of crops by enhancing yield to fulfill the increasing demand for food supply sustainably. The exploitation of genetic resources using genomics and metabolomics strategies can help generate resilient plants against stressors in the future. The innovation of the next-generation sequencing (NGS) strategies laid the foundation to unveil various plants' genetic potential and help us to understand the domestication process to unmask the genetic potential among wild-type plants to utilize for crop improvement. Nowadays, NGS is generating massive genomic resources using wild-type and domesticated plants grown under normal and harsh environments to explore the stress regulatory factors and determine the key metabolites. Improved food nutritional value is also the key to eradicating malnutrition problems around the globe, which could be attained by employing the knowledge gained through NGS and metabolomics to achieve suitability in crop yield. Advanced technologies can further enhance our understanding in defining the strategy to obtain a specific phenotype of a crop. Integration among bioinformatic tools and molecular techniques, such as marker-assisted, QTLs mapping, creation of reference genome, de novo genome assembly, pan- and/or super-pan-genomes, etc., will boost breeding programs. The current article provides sequential progress in NGS technologies, a broad application of NGS, enhancement of genetic manipulation resources, and understanding the crop response to stress by producing plant metabolites. The NGS and metabolomics utilization in generating stress-tolerant plants/crops without deteriorating a natural ecosystem is considered a sustainable way to improve agriculture production. This highlighted knowledge also provides useful research that explores the suitable resources for agriculture sustainability.
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Affiliation(s)
- Muhammad Furqan Ashraf
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Dan Hou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Quaid Hussain
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Muhammad Imran
- Colleges of Agriculture and Horticulture, South China Agricultural University, Guangzhou 510642, China; (M.I.); (M.W.)
| | - Jialong Pei
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Mohsin Ali
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Aamar Shehzad
- Maize Research Station, AARI, Faisalabad 38000, Pakistan;
| | - Muhammad Anwar
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China;
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad 38000, Pakistan;
| | - Muhammad Waseem
- Colleges of Agriculture and Horticulture, South China Agricultural University, Guangzhou 510642, China; (M.I.); (M.W.)
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
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Metabolomics and Molecular Approaches Reveal Drought Stress Tolerance in Plants. Int J Mol Sci 2021; 22:ijms22179108. [PMID: 34502020 PMCID: PMC8431676 DOI: 10.3390/ijms22179108] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 01/21/2023] Open
Abstract
Metabolic regulation is the key mechanism implicated in plants maintaining cell osmotic potential under drought stress. Understanding drought stress tolerance in plants will have a significant impact on food security in the face of increasingly harsh climatic conditions. Plant primary and secondary metabolites and metabolic genes are key factors in drought tolerance through their involvement in diverse metabolic pathways. Physio-biochemical and molecular strategies involved in plant tolerance mechanisms could be exploited to increase plant survival under drought stress. This review summarizes the most updated findings on primary and secondary metabolites involved in drought stress. We also examine the application of useful metabolic genes and their molecular responses to drought tolerance in plants and discuss possible strategies to help plants to counteract unfavorable drought periods.
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Gbashi S, Adebo O, Adebiyi JA, Targuma S, Tebele S, Areo OM, Olopade B, Odukoya JO, Njobeh P. Food safety, food security and genetically modified organisms in Africa: a current perspective. Biotechnol Genet Eng Rev 2021; 37:30-63. [PMID: 34309495 DOI: 10.1080/02648725.2021.1940735] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Moving forward from 2020, Africa faces an eminent challenge of food safety and security in the coming years. The World Food Programme (WFP) of the United Nations (UN) estimates that 20% of Africa's population of 1.2 billion people face the highest level of undernourishment in the world, likely to worsen due to COVID-19 pandemic that has brought the entire world to its knees. Factors such as insecurity and conflict, poverty, climate change and population growth have been identified as critical contributors to the food security challenges on the continent. Biotechnological research on Genetically Modified Organisms (GMOs) provides a range of opportunities (such as increased crop yields, resistance to pests and diseases, enhanced nutrient composition and food quality) in addressing the hunger, malnutrition and food security issues on the continent. However, the acceptance and adoption of GMOs on the continent has been remarkably slow, perhaps due to contrasting views about the benefits and safety concerns associated with them. With the reality of food insecurity and the booming population in Africa, there is an eminent need for a more pragmatic position to this debate. The present review presents an overview of the current situation of food safety and security and attempts to reconcile major viewpoints on GMOs research considering the current food safety and security crisis in the African continent.
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Affiliation(s)
- Sefater Gbashi
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, P.O Box 17011, Doornfontein Campus, 2028, Gauteng, South Africa
| | - Oluwafemi Adebo
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, P.O Box 17011, Doornfontein Campus, 2028, Gauteng, South Africa
| | - Janet Adeyinka Adebiyi
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, P.O Box 17011, Doornfontein Campus, 2028, Gauteng, South Africa
| | - Sarem Targuma
- Department of Chemical Sciences, Faculty of Science, University of Johannesburg, P.O Box 17011, Doornfontein Campus, 2028, Gauteng, South Africa
| | - Shandry Tebele
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch, 7701
| | - Oluwaseun Mary Areo
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, P.O Box 17011, Doornfontein Campus, 2028, Gauteng, South Africa
| | - Bunmi Olopade
- Department of Biological Sciences, Covenant University, Ota, P.M.B. 1023, km 10, Idiroko Road, Ota, Ogun State, Nigeria
| | - Julianah Olayemi Odukoya
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, P.O Box 17011, Doornfontein Campus, 2028, Gauteng, South Africa
| | - Patrick Njobeh
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, P.O Box 17011, Doornfontein Campus, 2028, Gauteng, South Africa
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10
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Medeiros DB, Brotman Y, Fernie AR. The utility of metabolomics as a tool to inform maize biology. PLANT COMMUNICATIONS 2021; 2:100187. [PMID: 34327322 PMCID: PMC8299083 DOI: 10.1016/j.xplc.2021.100187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/26/2021] [Accepted: 04/19/2021] [Indexed: 05/04/2023]
Abstract
With the rise of high-throughput omics tools and the importance of maize and its products as food and bioethanol, maize metabolism has been extensively explored. Modern maize is still rich in genetic and phenotypic variation, yielding a wide range of structurally and functionally diverse metabolites. The maize metabolome is also incredibly dynamic in terms of topology and subcellular compartmentalization. In this review, we examine a broad range of studies that cover recent developments in maize metabolism. Particular attention is given to current methodologies and to the use of metabolomics as a tool to define biosynthetic pathways and address biological questions. We also touch upon the use of metabolomics to understand maize natural variation and evolution, with a special focus on research that has used metabolite-based genome-wide association studies (mGWASs).
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Affiliation(s)
- David B. Medeiros
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
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11
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Pazhamala LT, Kudapa H, Weckwerth W, Millar AH, Varshney RK. Systems biology for crop improvement. THE PLANT GENOME 2021; 14:e20098. [PMID: 33949787 DOI: 10.1002/tpg2.20098] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/09/2021] [Indexed: 05/19/2023]
Abstract
In recent years, generation of large-scale data from genome, transcriptome, proteome, metabolome, epigenome, and others, has become routine in several plant species. Most of these datasets in different crop species, however, were studied independently and as a result, full insight could not be gained on the molecular basis of complex traits and biological networks. A systems biology approach involving integration of multiple omics data, modeling, and prediction of the cellular functions is required to understand the flow of biological information that underlies complex traits. In this context, systems biology with multiomics data integration is crucial and allows a holistic understanding of the dynamic system with the different levels of biological organization interacting with external environment for a phenotypic expression. Here, we present recent progress made in the area of various omics studies-integrative and systems biology approaches with a special focus on application to crop improvement. We have also discussed the challenges and opportunities in multiomics data integration, modeling, and understanding of the biology of complex traits underpinning yield and stress tolerance in major cereals and legumes.
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Affiliation(s)
- Lekha T Pazhamala
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Himabindu Kudapa
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology and School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
- State Agricultural Biotechnology Centre, Crop Research Innovation Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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12
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Emwas AHM, Al-Rifai N, Szczepski K, Alsuhaymi S, Rayyan S, Almahasheer H, Jaremko M, Brennan L, Lachowicz JI. You Are What You Eat: Application of Metabolomics Approaches to Advance Nutrition Research. Foods 2021; 10:1249. [PMID: 34072780 PMCID: PMC8229064 DOI: 10.3390/foods10061249] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 12/17/2022] Open
Abstract
A healthy condition is defined by complex human metabolic pathways that only function properly when fully satisfied by nutritional inputs. Poor nutritional intakes are associated with a number of metabolic diseases, such as diabetes, obesity, atherosclerosis, hypertension, and osteoporosis. In recent years, nutrition science has undergone an extraordinary transformation driven by the development of innovative software and analytical platforms. However, the complexity and variety of the chemical components present in different food types, and the diversity of interactions in the biochemical networks and biological systems, makes nutrition research a complicated field. Metabolomics science is an "-omic", joining proteomics, transcriptomics, and genomics in affording a global understanding of biological systems. In this review, we present the main metabolomics approaches, and highlight the applications and the potential for metabolomics approaches in advancing nutritional food research.
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Affiliation(s)
- Abdul-Hamid M. Emwas
- Imaging and Characterization Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Nahla Al-Rifai
- Environmental Technology Management (2005-2012), College for Women, Kuwait University, P.O. Box 5969, Safat 13060, Kuwait;
| | - Kacper Szczepski
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (S.A.); (M.J.)
| | - Shuruq Alsuhaymi
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (S.A.); (M.J.)
| | - Saleh Rayyan
- Chemistry Department, Birzeit University, Birzeit 627, Palestine;
| | - Hanan Almahasheer
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University (IAU), Dammam 31441-1982, Saudi Arabia;
| | - Mariusz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (S.A.); (M.J.)
| | - Lorraine Brennan
- Institute of Food and Health and Conway Institute, School of Agriculture & Food Science, Dublin 4, Ireland;
| | - Joanna Izabela Lachowicz
- Department of Medical Sciences and Public Health, University of Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy
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13
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Girón-Calva PS, Pérez-Fons L, Sandmann G, Fraser PD, Christou P. Nitrogen inputs influence vegetative metabolism in maize engineered with a seed-specific carotenoid pathway. PLANT CELL REPORTS 2021; 40:899-911. [PMID: 33787959 DOI: 10.1007/s00299-021-02689-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Metabolomic profiling of a maize line engineered with an endosperm-specific carotenogenic pathway revealed unexpected metabolic readjustments of primary metabolism in leaves and roots. High-carotenoid (HC) maize was engineered to accumulate high levels of carotenoids in the endosperm. The metabolic interventions influenced the flux through non-target pathways in tissues that were not affected by the targeted intervention. HC maize at the vegetative stage also showed a reduced susceptibility to insect feeding. It is unknown, however, whether the metabolic history of the embryo has any impact on the metabolite composition in vegetative tissues. We, therefore, compared HC maize and its isogenic counterpart (M37W) to test the hypothesis that boosting the carotenoid content in the endosperm triggers compensatory effects in core metabolism in vegetative tissues. Specifically, we investigated whether the metabolite composition of leaves and roots at the V6 stage differs between HC and M37W, and whether N inputs further alter the core metabolism of HC compared to M37W. We found an increase in the abundance of organic acids from the tricarboxylic acid (TCA) cycle in HC even under restricted N conditions. In contrast, low levels of carotenoids and chlorophyll were measured regardless of N levels. Sugars were also significantly depleted in HC under low N. We propose a model explaining the observed genotype-dependent and input-dependent effects, in which organic acids derived from the TCA cycle accumulate during vegetative growth and contribute to the increased demand for pyruvate and/or acetyl-CoA in the endosperm and embryo. This response may in part reflect the transgenerational priming of vegetative tissues in the embryo induced by the increased demand for metabolic precursors during seed development in the previous generation.
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Affiliation(s)
- Patricia S Girón-Calva
- Department of Plant Production and Forestry Sciences, University of Lleida-Agrotecnio Center, Lleida, Spain
| | - Laura Pérez-Fons
- Department of Biological Sciences, Royal Holloway, University London, Egham, Surrey, UK
| | - Gerhard Sandmann
- Institute of Molecular Bioscience, J. W. Goethe University, Frankfurt am Main, Germany
| | - Paul D Fraser
- Department of Biological Sciences, Royal Holloway, University London, Egham, Surrey, UK.
| | - Paul Christou
- Department of Plant Production and Forestry Sciences, University of Lleida-Agrotecnio Center, Lleida, Spain.
- ICREA, Catalan Institute for Research and Advanced Studies, Barcelona, Spain.
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14
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Metabolic Analysis Reveals Cry1C Gene Transformation Does Not Affect the Sensitivity of Rice to Rice Dwarf Virus. Metabolites 2021; 11:metabo11040209. [PMID: 33808359 PMCID: PMC8065979 DOI: 10.3390/metabo11040209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/22/2021] [Accepted: 03/29/2021] [Indexed: 12/16/2022] Open
Abstract
Metabolomics is beginning to be used for assessing unintended changes in genetically modified (GM) crops. To investigate whether Cry1C gene transformation would induce metabolic changes in rice plants, and whether the metabolic changes would pose potential risks when Cry1C rice plants are exposed to rice dwarf virus (RDV), the metabolic profiles of Cry1C rice T1C-19 and its non-Bt parental rice MH63 under RDV-free and RDV-infected status were analyzed using gas chromatography–mass spectrometry (GC-MS). Compared to MH63 rice, slice difference was detected in T1C-19 under RDV-free conditions (less than 3%), while much more metabolites showed significant response to RDV infection in T1C-19 (15.6%) and in MH63 (5.0%). Pathway analysis showed biosynthesis of lysine, valine, leucine, and isoleucine may be affected by RDV infection in T1C-19. No significant difference in the contents of free amino acids (AAs) was found between T1C-19 and MH63 rice, and the free AA contents of the two rice plants showed similar responses to RDV infection. Furthermore, no significant differences of the RDV infection rates between T1C-19 and MH63 were detected. Our results showed the Cry1C gene transformation did not affect the sensitivity of rice to RDV, indicating Cry1C rice would not aggravate the epidemic and dispersal of RDV.
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15
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Liu W, Chen H, Li L, Dong M, Zhang Z, Wan Y, Jin W. Proteomic analysis of the seeds of transgenic rice lines and the corresponding nongenetically modified isogenic variety. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:1869-1878. [PMID: 32898281 DOI: 10.1002/jsfa.10802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 08/23/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND An isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic analysis was employed to study the seeds of two genetically modified (GM) rice lines, T2A-1 and T1C-19, and their nontransgenic isogenic variety, MH63, to investigate the unintended effects of genetic modification. RESULTS A total of 3398 proteins were quantitatively identified. Seventy-seven differentially abundant proteins (DAPs) were identified in the T2A-1/MH63 comparison, and 70 and 7 of these DAPs were upregulated and downregulated, respectively. A pathway enrichment analysis showed that most of these DAPs participated in metabolic pathways and protein processing in endoplasmic reticulum and were ribosome components. Some 181 DAPs were identified from the T1C-19/MH63 comparison, and these included 115 upregulated proteins and 66 downregulated proteins. The subsequent pathway enrichment analysis showed that these DAPs mainly participated in protein processing in endoplasmic reticulum and carbon fixation in photosynthetic organisms and were ribosome components. None of these DAPs were identified as new unintended toxins or allergens, and only changes in abundance were detected. Fifty-four co-DAPs were identified in the seeds of the two GM rice lines, and protein-protein interaction analysis of these co-DAPs demonstrated that some interacting proteins were involved in protein processing in endoplasmic reticulum and metabolic pathways, whereas others were identified as ribosome components. Representative co-DAPs and proteins related to nutrients were analyzed using qRT-PCR to determine their transcriptional levels. CONCLUSIONS The results suggested that the seed proteomic profiles of the two GM rice lines studied were not substantially altered from those of their natural isogenic control. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Weixiao Liu
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, PR China
| | - Hao Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Liang Li
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, PR China
| | - Mei Dong
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, PR China
| | - Zhe Zhang
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, PR China
| | - Yusong Wan
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, PR China
| | - Wujun Jin
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, PR China
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16
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Boonchaisri S, Rochfort S, Stevenson T, Dias DA. LC-MS untargeted metabolomics assesses the delayed response of glufosinate treatment of transgenic glufosinate resistant (GR) buffalo grasses (Stenotaphrum secundatum L.). Metabolomics 2021; 17:28. [PMID: 33609206 DOI: 10.1007/s11306-021-01776-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 02/04/2021] [Indexed: 10/22/2022]
Abstract
INTRODUCTION Glufosinate resistant (GR) buffalo grasses were genetically modified to resist the broad-spectrum herbicide, glufosinate by inserting a novel pat gene into its genome. This modification results in a production of additional phosphinothricin acetyltransferase (PAT) to detoxify the deleterious effects of glufosinate. The GR grasses and its associated herbicide form a modern, weeding program, to eradicate obnoxious weeds in turf lawn without damaging the grasses at relatively low costs and labor. As with several principal crops which are genetically modified to improve agricultural traits, biosafety of the GR buffalo grasses is inevitably expected to become a public concern. For the first time, we had previously examined the metabolome of glufosinate-resistant buffalo grasses, using a GC-MS untargeted approach to assess the risk of GR as well as identify any pleotropic effects arising from the genetically modification process. In this paper, an untargeted high-resolution LC-MS (LC-HRMS) untargeted metabolomics approach was carried out to complement our previous findings with respect to GR and wild type (WT) buffalo grasses. OBJECTIVE One of the major aims of this present work was to compare GR to WT buffalo grasses by including the detection of the secondary metabolome and determine any unprecedented metabolic changes. METHODS Eight-week old plants of 4 GR buffalo grasses, (93-1A, 93-2B, 93-3 C and 93-5A) and 3 wild type varieties (WT 8-4A, WT 9-1B and WT 9-1B) were submerged in either 5 % v/v of glufosinate or distilled water 3 days prior to a LC-HRMS based untargeted metabolomics analysis (glufosinate-treated or control, samples, respectively). An Ultra-High-Performance Liquid Chromatography (UHPLC) system coupled to a Velos Pro Orbitrap mass spectrometer system was employed to holistically measure the primary and secondary metabolome of both GR and WT buffalo grasses either treated with or without glufosinate and subsequently apply several bioinformatic tools including the automated pathway analysis algorithm, mummichog. RESULTS LC-HRMS untargeted based metabolomics clearly identified that the global metabolite pools of both GR and WT cultivars were highly similar, providing strong, supporting evidence of substantial equivalence between the GR and WT varieties. These findings indicate that if any associated risks to these GR grasses were somehow present, the risk would be within those acceptable ranges present in the WT. Additionally, mummichog-based pathway analysis indicated that phenylalanine metabolism and the TCA cycle were significantly impacted by glufosinate treatment in the WT cultivar. It was possible that alterations in the relative concentrations of several intermediates in these pathways were likely due to glufosinate-induced production of secondary metabolites to enhance plant defense mechanisms against herbicidal stress at the expense of primary metabolism. CONCLUSIONS GR buffalo grasses were found to be near identical to its WT comparator based on this complementary LC-HRMS based untargeted metabolomics. Therefore, these results further support the safe use of these GR buffalo grasses with substantial evidence. Interestingly, despite protected by PAT, GR buffalo grasses still demonstrated the response to glufosinate treatment by up-regulating some secondary metabolite-related pathways.
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Affiliation(s)
- Siriwat Boonchaisri
- Division of Biology, School of Sciences, University of Phayao, Phayao, 56000, Thailand
- School of Science, RMIT University, Bundoora, VIC, 3083, Australia
| | - Simone Rochfort
- Agriculture Research Victoria, AgriBio, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Trevor Stevenson
- School of Science, RMIT University, Bundoora, VIC, 3083, Australia
| | - Daniel A Dias
- School of Health and Biomedical Sciences, Discipline of Laboratory Medicine, RMIT University, PO Box 71, Bundoora, VIC, 3083, Australia.
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17
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Fu W, Zhu P, Qu M, Zhi W, Zhang Y, Li F, Zhu S. Evaluation on reprogramed biological processes in transgenic maize varieties using transcriptomics and metabolomics. Sci Rep 2021; 11:2050. [PMID: 33479482 PMCID: PMC7820507 DOI: 10.1038/s41598-021-81637-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 12/16/2020] [Indexed: 11/12/2022] Open
Abstract
Genetic engineering (GM) has great potential to improve maize productivity, but rises some concerns on unintended effects, and equivalent as their comparators. There are some limitations through targeted analysis to detect the UE in genetically modified organisms in many previous studies. We here reported a case-study on the effects of introducing herbicides and insect resistance (HIR) gene cassette on molecular profiling (transcripts and metabolites) in a popular maize variety Zhengdan958 (ZD958) in China. We found that introducing HIR gene cassette bring a limited numbers of differential abundant genes (DAGs) or differential abundant metabolites (DAMs) between transgenic events and non-transgenic control. In contrast, averaged 10 times more DAGs and DAMs were observed when performed comparison under different growing environments in three different ecological regions of China than the numbers induced by gene effects. Major biological pathways relating to stress response or signaling transduction could explain somehow the effects of growing environments. We further compared two transgenic events mediated ZD958 (GM-ZD958) with either transgenic parent GM-Z58, and other genetic background nonGM-Z58, nonGM-ZD958, and Chang7-2. We found that the numbers of DAGs and DAMs between GM-ZD958 and its one parent maize variety, Z58 or GM-Z58 is equivalent, but not Chang7-2. These findings suggest that greater effects due to different genetic background on altered molecular profiling than gene modification itself. This study provides a case evidence indicating marginal effects of gene pleiotropic effects, and environmental effects should be emphasized.
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Affiliation(s)
- Wei Fu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Pengyu Zhu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Mingnan Qu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai, 200032, China
| | - Wang Zhi
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Yongjiang Zhang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Feiwu Li
- Institute of Agricultural Quality Standard and Testing Technology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin, China.
| | - Shuifang Zhu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China.
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18
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Jin L, Wang D, Mu Y, Guo Y, Lin Y, Qiu L, Pan Y. Proteomics analysis reveals that foreign cp4-epsps gene regulates the levels of shikimate and branched pathways in genetically modified soybean line H06-698. GM CROPS & FOOD 2021; 12:497-508. [PMID: 34984949 PMCID: PMC9208623 DOI: 10.1080/21645698.2021.2000320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/23/2021] [Accepted: 10/26/2021] [Indexed: 11/29/2022]
Abstract
Although genetically modified (GM) glyphosate-resistant soybeans with cp4-epsps gene have been widely planted all over the world, their proteomic characteristics are not very clear. In this study, the soybean seeds of a GM soybean line H06-698 (H) with cp4-epsps gene and its non-transgenic counterpart Mengdou12 (M), which were collected from two experiment fields in two years and used as 4 sample groups, were analyzed with label-free proteomics technique. A total of 1706 proteins were identified quantitatively by label-free quantification, and a total of 293 proteins were detected as common differential abundance proteins (DAPs, FC is not less than 1.5) both in two groups or more. Functional enrichment analysis of common DAPs identified from four groups, shows that most up-regulated proteins were clustered into stress response, carbon and energy metabolism, and genetic information processing. Further documentary analysis shows that 15 proteins play important roles in shikimate pathways, reactive oxygen species (ROS) and stress response. These results indicated that the change of protein abundance in different samples were affected by various factors, but except shikimate and branched pathways related proteins, only ROS and stress-related proteins were found to be stably regulated by cp4-epsps gene, and no unexpected and safety-related proteins such as antinutritional factors, allergenic proteins, and toxic proteins were found as DAPs. The influence of foreign genes in genetically modified plants is worthy of attention and this work provides new clues for exploring the regulated proteins and pathways in GM plants.
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Affiliation(s)
- Longguo Jin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Daoping Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongying Mu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yong Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yangjie Lin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijuan Qiu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yinghong Pan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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19
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Liu W, Zhao H, Miao C, Jin W. Integrated proteomics and metabolomics analysis of transgenic and gene-stacked maize line seeds. GM CROPS & FOOD 2021; 12:361-375. [PMID: 34097556 PMCID: PMC8189116 DOI: 10.1080/21645698.2021.1934351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Unintended effects of genetically modified (GM) crops may pose safety issues. Omics techniques provide researchers with useful tools to assess such unintended effects. Proteomics and metabolomics analyses were performed for three GM maize varieties, 2A-7, CC-2, and 2A-7×CC-2 stacked transgenic maize, and the corresponding non-GM parent Zheng58.Proteomics revealed 120, 271 and 135 maize differentially expressed proteins (DEPs) in the 2A-7/Zheng58, CC-2/Zheng58 and 2A-7×CC-2/Zheng58 comparisons, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that most DEPs participated in metabolic pathways and the biosynthesis of secondary metabolite. Metabolomics revealed 179, 135 and 131 differentially accumulated metabolites (DAMs) in the 2A-7/Zheng58, CC-2/Zheng58 and 2A-7×CC-2/Zheng58 comparisons, respectively. Based on KEGG enrichment analysis, most DAMs are involved in the biosynthesis of secondary metabolite and metabolic pathways. According to integrated proteomics and metabolomics analysis, the introduction of exogenous EPSPS did not affect the expression levels of six other enzymes or the abundance of seven metabolites involved in the shikimic acid pathway in CC-2 and 2A-7×CC-2 seeds. Six co-DEPs annotated by integrated proteomics and metabolomics pathway analysis were further analyzed by qRT-PCR.This study successfully employed integrated proteomic and metabolomic technology to assess unintended changes in maize varieties. The results suggest that GM and gene stacking do not cause significantly unintended effects.
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Affiliation(s)
- Weixiao Liu
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, P.R. China
| | - Haiming Zhao
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Chaohua Miao
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, P.R. China
| | - Wujun Jin
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, P.R. China
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Zhang X, Zhang R, Li L, Yang Y, Ding Y, Guan H, Wang X, Zhang A, Wen H. Negligible transcriptome and metabolome alterations in RNAi insecticidal maize against Monolepta hieroglyphica. PLANT CELL REPORTS 2020; 39:1539-1547. [PMID: 32869121 PMCID: PMC7554010 DOI: 10.1007/s00299-020-02582-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/17/2020] [Indexed: 06/01/2023]
Abstract
RNAi-based genetically modified maize resistant to Monolepta hieroglyphica (Motschulsky) was demonstrated with negligible transcriptome and metabolome alterations compared to its unmodified equivalent. As one of the most prevalent insect pests afflicting various crops, Monolepta hieroglyphica (Motschulsky) causes severe loss of agricultural and economic productivity for many years in China. In an effort to reduce damages, in this study, an RNA interference (RNAi)-based genetically modified (GM) maize was developed. It was engineered to produce MhSnf7 double-stranded RNAs (dsRNAs), which can suppress the Snf7 gene expression and then lead M. hieroglyphica to death. Field trail analysis confirmed the robustly insecticidal ability of the MhSnf7 GM maize to resist damages by M. hieroglyphica. RNA sequencing analysis identified that only one gene was differentially expressed in the MhSnf7 GM maize compared to non-GM maize, indicating that the transcriptome in MhSnf7 GM maize is principally unaffected by the introduction of the MhSnf7 dsRNA expression vector. Likewise, metabolomics analysis identified that only 8 out of 5787 metabolites were significantly changed. Hence, the integration of transcriptomics and metabolomics demonstrates that there are negligible differences between MhSnf7 GM maize and its unmodified equivalent. This study not only presents a comprehensive assessment of cellular alteration in terms of gene transcription and metabolite abundance in RNAi-based GM maize, but also could be used as a reference for evaluating the unintended effect of GM crops.
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Affiliation(s)
- Xiaolei Zhang
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Ruiying Zhang
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Liang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yang Yang
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Yijia Ding
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Haitao Guan
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Xiaoqin Wang
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Aihong Zhang
- Beijing DaBeiNong Biotechnology Co., Ltd., Beijing, 100080, China
| | - Hongtao Wen
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China.
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21
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iTRAQ-based quantitative proteomic analysis of transgenic and non-transgenic maize seeds. J Food Compost Anal 2020. [DOI: 10.1016/j.jfca.2020.103564] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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22
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Metabolomics: A Tool for Cultivar Phenotyping and Investigation of Grain Crops. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10060831] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The quality of plants is often enhanced for diverse purposes such as improved resistance to environmental pressures, better taste, and higher yields. Considering the world’s dependence on plants (nutrition, medicine, or biofuel), developing new cultivars with superior characteristics is of great importance. As part of the ‘omics’ approaches, metabolomics has been employed to investigate the large number of metabolites present in plant systems under well-defined environmental conditions. Recent advances in the metabolomics field have greatly expanded our understanding of plant metabolism, largely driven by potential application to agricultural systems. The current review presents the workflow for plant metabolome analyses, current knowledge, and future directions of such research as determinants of cultivar phenotypes. Furthermore, the value of metabolome analyses in contemporary crop science is illustrated. Here, metabolomics has provided valuable information in research on grain crops and identified significant biomarkers under different conditions and/or stressors. Moreover, the value of metabolomics has been redefined from simple biomarker identification to a tool for discovering active drivers involved in biological processes. We illustrate and conclude that the rapid advances in metabolomics are driving an explosion of information that will advance modern breeding approaches for grain crops and address problems associated with crop productivity and sustainable agriculture.
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Coumoul X, Servien R, Juricek L, Kaddouch-Amar Y, Lippi Y, Berthelot L, Naylies C, Morvan ML, Antignac JP, Desdoits-Lethimonier C, Jegou B, Tremblay-Franco M, Canlet C, Debrauwer L, Le Gall C, Laurent J, Gouraud PA, Cravedi JP, Jeunesse E, Savy N, Dandere-Abdoulkarim K, Arnich N, Fourès F, Cotton J, Broudin S, Corman B, Moing A, Laporte B, Richard-Forget F, Barouki R, Rogowsky P, Salles B. The GMO90+ Project: Absence of Evidence for Biologically Meaningful Effects of Genetically Modified Maize-based Diets on Wistar Rats After 6-Months Feeding Comparative Trial. Toxicol Sci 2020; 168:315-338. [PMID: 30535037 PMCID: PMC6432862 DOI: 10.1093/toxsci/kfy298] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The GMO90+ project was designed to identify biomarkers of exposure or health effects in Wistar Han RCC rats exposed in their diet to 2 genetically modified plants (GMP) and assess additional information with the use of metabolomic and transcriptomic techniques. Rats were fed for 6-months with 8 maize-based diets at 33% that comprised either MON810 (11% and 33%) or NK603 grains (11% and 33% with or without glyphosate treatment) or their corresponding near-isogenic controls. Extensive chemical and targeted analyses undertaken to assess each diet demonstrated that they could be used for the feeding trial. Rats were necropsied after 3 and 6 months. Based on the Organization for Economic Cooperation and Development test guideline 408, the parameters tested showed a limited number of significant differences in pairwise comparisons, very few concerning GMP versus non-GMP. In such cases, no biological relevance could be established owing to the absence of difference in biologically linked variables, dose-response effects, or clinical disorders. No alteration of the reproduction function and kidney physiology was found. Metabolomics analyses on fluids (blood, urine) were performed after 3, 4.5, and 6 months. Transcriptomics analyses on organs (liver, kidney) were performed after 3 and 6 months. Again, among the significant differences in pairwise comparisons, no GMP effect was observed in contrast to that of maize variety and culture site. Indeed, based on transcriptomic and metabolomic data, we could differentiate MON- to NK-based diets. In conclusion, using this experimental design, no biomarkers of adverse health effect could be attributed to the consumption of GMP diets in comparison with the consumption of their near-isogenic non-GMP controls.
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Affiliation(s)
- Xavier Coumoul
- INSERM UMR-S1124, Toxicologie Pharmacologie et Signalisation Cellulaire, Université Paris Descartes, USPC, Paris, France
| | - Rémi Servien
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Ludmila Juricek
- INSERM UMR-S1124, Toxicologie Pharmacologie et Signalisation Cellulaire, Université Paris Descartes, USPC, Paris, France
| | - Yael Kaddouch-Amar
- INSERM UMR-S1124, Toxicologie Pharmacologie et Signalisation Cellulaire, Université Paris Descartes, USPC, Paris, France
| | - Yannick Lippi
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Laureline Berthelot
- Centre de Recherche sur l'Inflammation (CRI), INSERM UMRS 1149, Paris, France
| | - Claire Naylies
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | | | | | | | - Bernard Jegou
- Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), Université de Rennes, Rennes, France
| | - Marie Tremblay-Franco
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Cécile Canlet
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Laurent Debrauwer
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | | | | | | | - Jean-Pierre Cravedi
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Elisabeth Jeunesse
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Nicolas Savy
- Institut de Mathématiques de Toulouse, UMR5219-Université de Toulouse, CNRS-UPS IMT, Toulouse, France
| | | | | | | | | | | | | | - Annick Moing
- UMR1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Villenave d'Ornon, France
| | - Bérengère Laporte
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | | | - Robert Barouki
- INSERM UMR-S1124, Toxicologie Pharmacologie et Signalisation Cellulaire, Université Paris Descartes, USPC, Paris, France
| | - Peter Rogowsky
- Laboratoire Reproduction et Développement des Plantes, CNRS, INRA, University Lyon, Lyon, France
| | - Bernard Salles
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
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Boonchaisri S, Stevenson T, Dias DA. Utilization of GC-MS untargeted metabolomics to assess the delayed response of glufosinate treatment of transgenic herbicide resistant (HR) buffalo grasses (Stenotaphrum secundatum L.). Metabolomics 2020; 16:22. [PMID: 31989303 DOI: 10.1007/s11306-020-1644-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 01/22/2020] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Herbicide resistant (HR) buffalo grasses were genetically engineered to resist the non-selective herbicide, glufosinate in order to facilitate a modern, 'weeding program' which is highly effective in terms of minimizing costs and labor. The resistant trait was conferred by an insertion of the pat gene to allow for the production of the enzyme phosphinothricin acetyltransferase (PAT) to detoxify the glufosinate inhibitive effect. To date, there are only a few reports using metabolomics as well as molecular characterizations published for glufosinate-resistant crops with no reports on HR turfgrass. Therefore, for the first time, this study examines the metabolome of glufosinate-resistant buffalo grasses which not only will be useful to future growers but also the scientific community. OBJECTIVE A major aim of this present work is to characterize and evaluate the metabolic alterations which may arise from a genetic transformation of HR buffalo grasses by comprehensively using gas chromatography-mass spectrometry (GC-MS) based untargeted metabolomics. METHODS Eight-week old plants of 4 HR buffalo grasses, (93-1A, 93-2B, 93-3C and 93-5A) and 3 wild type varieties (WT 8-4A, WT 9-1B and WT 9-1B) were selected for physiological, molecular and metabolomics experiments. Plants were either sprayed with 1, 5, 10 and 15% v/v of glufosinate to evaluate the visual injuries or submerged in 5% v/v of glufosinate 3 days prior to a GC-MS based untargeted metabolomics analysis. In contrast, the control group was treated with distilled water. Leaves were extracted in 1:1 methanol:water and then analysed, using an in-house GC-MS untargeted workflow. RESULTS Results identified 199 metabolites with only 6 of them (cis-aconitic acid, allantoin, cellobiose, glyceric acid, maltose and octadecanoic acid) found to be statistically significant (p < 0.05) between the HR and wild type buffalo grass varieties compared to the control experiment. Among these metabolites, unusual accumulation of allantoin was prominent and was an unanticipated effect of the pat gene insertion. As expected, glufosinate treatment caused significant metabolic alterations in the sensitive wild type, with the up-regulation of several amino acids (e.g. phenylalanine and isoleucine) which was likely due to glufosinate-induced senescence. The aminoacyl-tRNA biosynthetic pathway was identified as the most significant enriched pathway as a result of glufosinate effects because a number of its intermediates were amino acids. CONCLUSION HR buffalo grasses were very similar to its wild type comparator based on a comprehensive GC-MS based untargeted metabolomics and therefore, should guarantee the safe use of these HR buffalo grasses. The current metabolomics analyses not only confirmed the effects of glufosinate to up-regulate free amino acid pools in the sensitive wild type but also several alterations in sugar, sugar phosphate and organic acid metabolism have been reported.
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Affiliation(s)
| | - Trevor Stevenson
- School of Science, RMIT University, Bundoora, VIC, 3083, Australia
| | - Daniel A Dias
- School of Health and Biomedical Sciences, Discipline of Laboratory Medicine, RMIT University, PO Box 71, Bundoora, VIC, 3083, Australia.
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Chin EL, Ramsey JS, Mishchuk DO, Saha S, Foster E, Chavez JD, Howe K, Zhong X, Polek M, Godfrey KE, Mueller LA, Bruce JE, Heck M, Slupsky CM. Longitudinal Transcriptomic, Proteomic, and Metabolomic Analyses of Citrus sinensis (L.) Osbeck Graft-Inoculated with " Candidatus Liberibacter asiaticus". J Proteome Res 2020; 19:719-732. [PMID: 31885275 DOI: 10.1021/acs.jproteome.9b00616] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
"Candidatus Liberibacter asiaticus" (CLas) is the bacterium associated with the citrus disease Huanglongbing (HLB). Current CLas detection methods are unreliable during presymptomatic infection, and understanding CLas pathogenicity to help develop new detection techniques is challenging because CLas has yet to be isolated in pure culture. To understand how CLas affects citrus metabolism and whether infected plants produce systemic signals that can be used to develop improved detection techniques, leaves from Washington Navel orange (Citrus sinensis (L.) Osbeck) plants were graft-inoculated with CLas and longitudinally studied using transcriptomics (RNA sequencing), proteomics (liquid chromatography-tandem mass spectrometry), and metabolomics (proton nuclear magnetic resonance). Photosynthesis gene expression and protein levels were lower in infected plants compared to controls during late infection, and lower levels of photosynthesis proteins were identified as early as 8 weeks post-grafting. These changes coordinated with higher sugar concentrations, which have been shown to accumulate during HLB. Cell wall modification and degradation gene expression and proteins were higher in infected plants during late infection. Changes in gene expression and proteins related to plant defense were observed in infected plants as early as 8 weeks post-grafting. These results reveal coordinated changes in greenhouse navel leaves during CLas infection at the transcript, protein, and metabolite levels, which can inform of biomarkers of early infection.
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Affiliation(s)
- Elizabeth L Chin
- Department of Food Science and Technology , University of California, Davis , Davis , California 95616 , United States
| | - John S Ramsey
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health , USDA Agricultural Research Service , Ithaca , New York 14853 , United States.,Boyce Thompson Institute for Plant Research , Ithaca , New York 14853 , United States
| | - Darya O Mishchuk
- Department of Food Science and Technology , University of California, Davis , Davis , California 95616 , United States
| | - Surya Saha
- Boyce Thompson Institute for Plant Research , Ithaca , New York 14853 , United States
| | - Elizabeth Foster
- Contained Research Facility , University of California, Davis , Davis , California 95616 , United States
| | - Juan D Chavez
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Kevin Howe
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health , USDA Agricultural Research Service , Ithaca , New York 14853 , United States.,Boyce Thompson Institute for Plant Research , Ithaca , New York 14853 , United States
| | - Xuefei Zhong
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - MaryLou Polek
- National Clonal Germplasm Repository for Citrus & Dates , Riverside , California 92507 , United States
| | - Kris E Godfrey
- Contained Research Facility , University of California, Davis , Davis , California 95616 , United States
| | - Lukas A Mueller
- Boyce Thompson Institute for Plant Research , Ithaca , New York 14853 , United States
| | - James E Bruce
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Michelle Heck
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health , USDA Agricultural Research Service , Ithaca , New York 14853 , United States.,Boyce Thompson Institute for Plant Research , Ithaca , New York 14853 , United States.,Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science , Cornell University , Ithaca , New York 14853 , United States
| | - Carolyn M Slupsky
- Department of Food Science and Technology , University of California, Davis , Davis , California 95616 , United States
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Nur Sudrajat AB, Sugiharto B. Comparative Evaluation of Nutritional and Mineral Composition Between Transgenic Sugarcane Overexpressing SoSPS 1 Gene and Non-transgenic Counterpart. Pak J Biol Sci 2020; 23:1424-1430. [PMID: 33274870 DOI: 10.3923/pjbs.2020.1424.1430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND OBJECTIVE The high sucrose yield of transgenic sugarcane has been developed through the overexpression of gene for sucrose-phosphate synthase. Modification of the genome may result in alteration of biochemical profiles. This study was conducted to compare and evaluate the nutritional and mineral compositions between the transgenic and non-transgenic (NT) sugarcane counterpart. MATERIALS AND METHODS Four of transgenic lines with overexpressing SoSPS 1 gene and NT sugarcane were grown in greenhouse for 11 months. The nutritional and mineral compositions from leaves and stems were analyzed at the harvest. RESULTS Results revealed no significant differences in moisture, carbohydrates, crude fat and ash content between the transgenic lines and NT sugarcane. Protein and nitrogen contents were found to be significantly greater in steam of transgenic lines SP1 and SP3, including potassium content in both of the leaves and stems of transgenic lines. Although, the nutritional and mineral compositions were varied but their contents still within the range of Organization for Economic Co-operation and Development (OECD) reference values. CONCLUSION The results indicated that the nutritional and mineral compositions are substantially equivalent between transgenic and NT sugarcane.
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Liu W, Zhang Z, Liu X, Jin W. iTRAQ-based quantitative proteomic analysis of two transgenic soybean lines and the corresponding non-genetically modified isogenic variety. J Biochem 2020; 167:67-78. [PMID: 31596463 DOI: 10.1093/jb/mvz081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 09/27/2019] [Indexed: 11/14/2022] Open
Abstract
To investigate the unintended effects of genetically modified (GM) crops, an isobaric tags for relative and absolute quantitation (iTRAQ)-based comparative proteomic analysis was performed with seed cotyledons of two GM soybean lines, MON87705 and MON87701×MON89788, and the corresponding non-transgenic isogenic variety A3525. Thirty-five differentially abundant proteins (DAPs) were identified in MON87705/A3525, 27 of which were upregulated and 8 downregulated. Thirty-eight DAPs were identified from the MON87701×MON89788/A3525 sample, including 29 upregulated proteins and 9 downregulated proteins. Pathway analysis showed that most of these DAPs participate in protein processing in endoplasmic reticulum and in metabolic pathways. Protein-protein interaction analysis of these DAPs demonstrated that the main interacting proteins are associated with post-translational modification, protein turnover, chaperones and signal transduction mechanisms. Nevertheless, these DAPs were not identified as new unintended toxins or allergens and only showed changes in abundance. All these results suggest that the seed cotyledon proteomic profiles of the two GM soybean lines studied were not dramatically altered compared with that of their natural isogenic control.
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Affiliation(s)
- Weixiao Liu
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, No. 12 Zhongguancun South St., Haidian District, Beijing, P.R. China
| | - Zhe Zhang
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, No. 12 Zhongguancun South St., Haidian District, Beijing, P.R. China
| | - Xuri Liu
- Department of Food and Biological Engineering, Handan Polytechnic College, No.141 Zhuhe Road, Hanshan District, Handan, P.R. China
| | - Wujun Jin
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, No. 12 Zhongguancun South St., Haidian District, Beijing, P.R. China
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Pruter LS, Brewer MJ, Weaver MA, Murray SC, Isakeit TS, Bernal JS. Association of Insect-Derived Ear Injury With Yield and Aflatoxin of Maize Hybrids Varying in Bt Transgenes. ENVIRONMENTAL ENTOMOLOGY 2019; 48:1401-1411. [PMID: 31586402 DOI: 10.1093/ee/nvz112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Indexed: 06/10/2023]
Abstract
Environmental factors have been associated with the production of aflatoxin in maize, Zea mays L., and it is inconclusive whether transgenic, Bacillus thuringiensis (Bt), maize has an impact on aflatoxin accumulation. Maize hybrids differing in transgenes were planted in two locations from 2014 to 2017. Yield, aflatoxin, and ear injury caused by corn earworm, Helicoverpa zea (Boddie), and fall armyworm, Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae), were measured across three groups of hybrids differing in transgenes including near-isogenic hybrids, and water-stressed conditions. The hybrid groups consisted of non-Bt hybrids with no Bt transgenes, a second group with one or more Cry-Bt transgenes, and the third group with vegetative insecticidal Bt protein and Cry-Bt transgenes (Cry/Vip-Bt). Across the six data sets derived from 11 experiments, the Cry-Bt and Cry/Vip-Bt hybrids had less ear injury and aflatoxin on average than non-Bt hybrids. The effects of ear injury on yield and aflatoxin were more prominent and consistent in Corpus Christi, TX, where hybrids experienced more water-limited conditions than in College Station, TX. The trend of increased aflatoxin among hybrids with increased ear injury was further resolved when looking at Cry-Bt and Cry/Vip-Bt isogenic hybrids in Corpus Christi. The results supported that the maize hybrids with the inclusion of Cry-Bt and Cry/Vip-Bt transgenes warrant further investigation in an integrated approach to insect and aflatoxin management in sub-tropical rain-fed maize production regions. Research outcomes may be improved by focusing on areas prone to water-stress and by using hybrids with similar genetic backgrounds.
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Affiliation(s)
- Luke S Pruter
- Entomology Program, Texas A&M AgriLife Research & Extension Center, Corpus Christi, TX
| | - Michael J Brewer
- Entomology Program, Texas A&M AgriLife Research & Extension Center, Corpus Christi, TX
| | - Mark A Weaver
- Department of Plant Pathology, USDA-ARS, Stoneville, MS
| | - Seth C Murray
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX
| | - Thomas S Isakeit
- Department of Plant Pathology, Texas A&M University, College Station, TX
| | - Julio S Bernal
- Department of Entomology, Texas A&M University, College Station, TX
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Corujo M, Pla M, van Dijk J, Voorhuijzen M, Staats M, Slot M, Lommen A, Barros E, Nadal A, Puigdomènech P, Paz JLL, van der Voet H, Kok E. Use of omics analytical methods in the study of genetically modified maize varieties tested in 90 days feeding trials. Food Chem 2019; 292:359-371. [DOI: 10.1016/j.foodchem.2018.05.109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/04/2018] [Accepted: 05/24/2018] [Indexed: 10/16/2022]
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Wang X, Zhang X, Yang J, Liu X, Song Y, Wang Z. Genetic variation assessment of stacked-trait transgenic maize via conventional breeding. BMC PLANT BIOLOGY 2019; 19:346. [PMID: 31391002 PMCID: PMC6686426 DOI: 10.1186/s12870-019-1956-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/31/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND The safety assessment and control of stacked transgenic crops is increasingly important due to continuous crop development and is urgently needed in China. The genetic stability of foreign genes and unintended effects are the primary problems encountered in safety assessment. Omics techniques are useful for addressing these problems. The stacked transgenic maize variety 12-5 × IE034, which has insect-resistant and glyphosate-tolerant traits, was developed via a breeding stack using 12-5 and IE034 as parents. Using 12-5 × IE034, its parents (12-5 and IE034), and different maize varieties as materials, we performed proteomic profiling, molecular characterization and a genetic stability analysis. RESULTS Our results showed that the copy number of foreign genes in 12-5 × IE034 is identical to that of its parents 12-5 and IE034. Foreign genes can be stably inherited over different generations. Proteomic profiling analysis found no newly expressed proteins in 12-5 × IE034, and the differences in protein expression between 12 and 5 × IE034 and its parents were within the range of variation of conventional maize varieties. The expression levels of key enzymes participating in the shikimic acid pathway which is related to glyphosate tolerance of 12-5 × IE034 were not significantly different from those of its parents or five conventional maize varieties, which indicated that without selective pressure by glyphosate, the introduced EPSPS synthase is not has a pronounced impact on the synthesis of aromatic amino acids in maize. CONCLUSIONS Stacked-trait development via conventional breeding did not have an impact on the genetic stability of T-DNA, and the impact of stacked breeding on the maize proteome was less significant than that of genotypic differences. The results of this study provide a theoretical basis for the development of a safety assessment approach for stacked-trait transgenic crops in China.
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Affiliation(s)
- Xujing Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, 12 Zhuangguancun South Street, Beijing, 100081 China
| | - Xin Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, 12 Zhuangguancun South Street, Beijing, 100081 China
| | - Jiangtao Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, 12 Zhuangguancun South Street, Beijing, 100081 China
| | - Xiaojing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, 12 Zhuangguancun South Street, Beijing, 100081 China
| | - Yaya Song
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, 12 Zhuangguancun South Street, Beijing, 100081 China
| | - Zhixing Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, 12 Zhuangguancun South Street, Beijing, 100081 China
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Fu W, Wang C, Xu W, Zhu P, Lu Y, Wei S, Wu X, Wu Y, Zhao Y, Zhu S. Unintended effects of transgenic rice revealed by transcriptome and metabolism. GM CROPS & FOOD 2019; 10:20-34. [PMID: 30955410 DOI: 10.1080/21645698.2019.1598215] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Genetically modified (GM) organisms have been developed for decades. However, unintended effects are the main concerns of safety assessment that needs to be carefully investigated. Here, eight varieties of GM rice that were developed in China were selected to assess the unintended effects through transcriptome and metabolism. There are 2892-8758 differentially expressed genes (DEGs) and 7-50 metabolites at significant level between GM varieties and their isogenic counterparts, which were far fewer than that between traditional rice varieties. The function enrichment analysis showed altered transcription in stress-related pathway and starch and sucrose metabolism. DEGs shared among eight GM samples constitute less than 1% of the genes in the genome, and none of them is reported more than four times. The insertion effect on the nearby gene expression and the associated metabolism is only restricted to 50 genes. All the results provide a comprehensive analysis of unintended effects and indication of difference in Chinese transgenic rice based on their backgrounds, transformation, and insertion elements.
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Affiliation(s)
- Wei Fu
- a Chinese Academy of Inspection and Quarantine , Beijing , China
| | - Chenguang Wang
- a Chinese Academy of Inspection and Quarantine , Beijing , China.,b Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences , China Agricultural University , Beijing , China.,c College of Plant Protection , China Agricultural University , Beijing , China
| | - Wenjie Xu
- a Chinese Academy of Inspection and Quarantine , Beijing , China.,b Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences , China Agricultural University , Beijing , China.,c College of Plant Protection , China Agricultural University , Beijing , China
| | - Pengyu Zhu
- a Chinese Academy of Inspection and Quarantine , Beijing , China
| | - Yun Lu
- a Chinese Academy of Inspection and Quarantine , Beijing , China
| | - Shuang Wei
- d Guangdong Entry-Exit Inspection and Quarantine Bureau , Guangzhou , China
| | - Xiyang Wu
- e Department of Food Science and Engineering , Jinan University , Guangzhou , China
| | - Yuping Wu
- a Chinese Academy of Inspection and Quarantine , Beijing , China
| | - Yiqiang Zhao
- b Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences , China Agricultural University , Beijing , China
| | - Shuifang Zhu
- a Chinese Academy of Inspection and Quarantine , Beijing , China.,c College of Plant Protection , China Agricultural University , Beijing , China
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Boonchaisri S, Rochfort S, Stevenson T, Dias DA. Recent developments in metabolomics-based research in understanding transgenic grass metabolism. Metabolomics 2019; 15:47. [PMID: 30877485 DOI: 10.1007/s11306-019-1507-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 03/05/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Transgenic herbicide-resistant (HR) turfgrass together with its associated, broad spectrum herbicides promise cheap, selective and efficient weed control by excluding infested weeds resulting in turf lawn with high uniformity and aesthetic value. The concept of this "weeding program" initiated from modern biotechnology has been widely implemented in several principal crops including maize, soybean, canola and cotton as early as the 1990s. Transgenic HR turfgrass classified as a genetically modified organism (GMO) has undoubtedly caused public concern with respect to its biosafety and legalities similar to well-established HR crops. Nevertheless, applying metabolomics-based approaches which focuses on the identification of the global metabolic state of a biological system in response to either internal or external stimuli can also provide a comprehensive characterization of transgenic grass metabolism and its involvement in biosecurity and public perception. AIM OF REVIEW This review summaries the recent applications of metabolomics applied to HR crops to predict the molecular and physiological phenotypes of HR turfgrass species, glyphosate-resistant Kentucky bluegrass (Poa pratensis L.) and glufosinate-resistant creeping bentgrass (Agrotis stonifera L.). Additionally, this review also presents background knowledge with respect to the application of metabolomics, transformation of HR crops and its biosafety concerns, turfgrass botanical knowledge and its economic and aesthetic value. KEY SCIENTIFIC CONCEPTS OF REVIEW The purpose of this review is to demonstrate the molecular and physiological phenotypes of HR turfgrass based on several lines of evidence primarily derived from metabolomics data applied to HR crops to identify alterations on HR turfgrass metabolism as a result of genetic modification that confers resistant traits.
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Affiliation(s)
| | - Simone Rochfort
- Agriculture Research Victoria, AgriBio, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Trevor Stevenson
- School of Science, RMIT University, Bundoora, VIC, 3083, Australia
| | - Daniel A Dias
- School of Health and Biomedical Sciences, Discipline of Laboratory Medicine, RMIT University, PO Box 71, Bundoora, VIC, 3083, Australia.
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Recent Advances in MS-Based Plant Proteomics: Proteomics Data Validation Through Integration with Other Classic and -Omics Approaches. PROGRESS IN BOTANY 2019. [DOI: 10.1007/124_2019_32] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Liu W, Xu W, Li L, Dong M, Wan Y, He X, Huang K, Jin W. iTRAQ-based quantitative tissue proteomic analysis of differentially expressed proteins (DEPs) in non-transgenic and transgenic soybean seeds. Sci Rep 2018; 8:17681. [PMID: 30518773 PMCID: PMC6281665 DOI: 10.1038/s41598-018-35996-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 11/12/2018] [Indexed: 12/29/2022] Open
Abstract
The unintended effects of transgenesis have increased food safety concerns, meriting comprehensive evaluation. Proteomic profiling provides an approach to directly assess the unintended effects. Herein, the isobaric tags for relative and absolute quantitation (iTRAQ) comparative proteomic approach was employed to evaluate proteomic profile differences in seed cotyledons from 4 genetically modified (GM) and 3 natural genotypic soybean lines. Compared with their non-GM parents, there were 67, 61, 13 and 22 differentially expressed proteins (DEPs) in MON87705, MON87701 × MON89788, MON87708, and FG72. Overall, 170 DEPs were identified in the 3 GM soybean lines with the same parents, but 232 DEPs were identified in the 3 natural soybean lines. Thus, the differences in protein expression among the genotypic varieties were greater than those caused by GM. When considering ≥2 replicates, 4 common DEPs (cDEPs) were identified in the 3 different GM soybean lines with the same parents and 6 cDEPs were identified in the 3 natural varieties. However, when considering 3 replicates, no cDEPs were identified. Regardless of whether ≥2 or 3 replicates were considered, no cDEPs were identified among the 4 GM soybean lines. Therefore, no feedback due to GM was observed at the common protein level in this study.
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Affiliation(s)
- Weixiao Liu
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, 100081, PR China
| | - Wentao Xu
- Laboratory of Food Safety and Molecular Biology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, PR China
| | - Liang Li
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, 100081, PR China
| | - Mei Dong
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, 100081, PR China
| | - Yusong Wan
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, 100081, PR China
| | - Xiaoyun He
- Laboratory of Food Safety and Molecular Biology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, PR China
| | - Kunlun Huang
- Laboratory of Food Safety and Molecular Biology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, PR China.
| | - Wujun Jin
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, 100081, PR China.
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Rapid Identification of Genetically Modified Maize Using Laser-Induced Breakdown Spectroscopy. FOOD BIOPROCESS TECH 2018. [DOI: 10.1007/s11947-018-2216-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Agapito-Tenfen SZ, Vilperte V, Traavik TI, Nodari RO. Systematic miRNome profiling reveals differential microRNAs in transgenic maize metabolism. ENVIRONMENTAL SCIENCES EUROPE 2018; 30:37. [PMID: 30294516 PMCID: PMC6153861 DOI: 10.1186/s12302-018-0168-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND While some genetically modified organisms (GMOs) are created to produce new double-stranded RNA molecules (dsRNA), in others, such molecules may occur as an unintended effect of the genetic engineering process. Furthermore, GMOs might produce naturally occurring dsRNA molecules in higher or lower quantities than its non-transgenic counterpart. This study is the first to use high-throughput technology to characterize the miRNome of commercialized GM maize events and to investigate potential alterations in miRNA regulatory networks. RESULTS Thirteen different conserved miRNAs were found to be dys-regulated in GM samples. The insecticide Bt GM variety had the most distinct miRNome. These miRNAs target a range of endogenous transcripts, such as transcription factors and nucleic acid binding domains, which play key molecular functions in basic genetic regulation. In addition, we have identified 20 potential novel miRNAs with target transcripts involved in lipid metabolism in maize. isomiRs were also found in 96 conserved miRNAs sequences, as well as potential transgenic miRNA sequences, which both can be a source of potential off-target effects in the plant genome. We have also provided information on technical limitations and when to carry on additional in vivo experimental testing. CONCLUSIONS These findings do not reveal hazards per se but show that robust and reproducible miRNA profiling technique can strengthen the assessment of risk by detecting any new intended and unintended dsRNA molecules, regardless of the outcome, at any stage of GMO development.
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Affiliation(s)
| | - Vinicius Vilperte
- Departamento de Fitotecnia, Universidade Federal de Santa Catarina, Florianópolis, 88034000 Brazil
- Present Address: Institute for Plant Genetics, Faculty of Natural Sciences, Leibniz University of Hannover, 30419 Hannover, Germany
| | - Terje Ingemar Traavik
- GenØk–Centre for Biosafety, Forskningsparken i Breivika, Sykehusveien 23, 9294 Tromsø, Norway
| | - Rubens Onofre Nodari
- Departamento de Fitotecnia, Universidade Federal de Santa Catarina, Florianópolis, 88034000 Brazil
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Antoniou MN, Mesnage R, Agapito-Tenfen S, Séralini GE. Reply to 'Comments on two recent publications on GM maize and Roundup'. Sci Rep 2018; 8:13339. [PMID: 30177789 PMCID: PMC6120931 DOI: 10.1038/s41598-018-30751-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 07/30/2018] [Indexed: 11/09/2022] Open
Abstract
The opinion expressed by Eriksson and colleagues' fails to recognise that there are no standard experimental designs for academic investigations involving omics analyses of genetically modified crops and that the only valid comparator to determine the effect of the process of transgenesis is a near isogenic variety grown at the same time and location, as was the case in our investigation of NK603 maize. Eriksson does not acknowledge that the quality of the rat liver tissues in our chronic Roundup toxicity study has neither been questioned nor branded as unsuitable for further investigation. In addition, Eriksson fails to appreciate that the statistical methods we used to analyse the liver metabolomics dataset are recognised as appropriate as some of a number of approaches that can be taken. Moreover, Eriksson neglects to mention that the proteomics analysis of the liver tissues highlights structural and functional damage from Roundup exposure. Thus our results are sound and the claims by Eriksson and colleagues of experimental flaws are unfounded.Replying to: Eriksson et al. Sci Rep 8 (2018); https://doi.org/10.1038/s41598-018-30440-7 .
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Affiliation(s)
- Michael N Antoniou
- Gene Expression and Therapy Group, King's College London, Faculty of Life Sciences & Medicine, Department of Medical and Molecular Genetics, 8th Floor, Tower Wing, Guy's Hospital, Great Maze Pond, London, SE1 9RT, United Kingdom.
| | - Robin Mesnage
- Gene Expression and Therapy Group, King's College London, Faculty of Life Sciences & Medicine, Department of Medical and Molecular Genetics, 8th Floor, Tower Wing, Guy's Hospital, Great Maze Pond, London, SE1 9RT, United Kingdom
| | - Sarah Agapito-Tenfen
- Genøk, Center for Biosafety, The Science Park, P.O. Box 6418, Tromsø, 9294, Norway
- CropScience Department, Federal University of Santa Catarina, Rod. Admar Gonzaga 1346, 88034-000, Florianópolis, Brazil
| | - Gilles-Eric Séralini
- University of Caen, Institute of Biology, EA 2608 and Network on Risks, Quality and Sustainable Environment, MRSH, Esplanade de la Paix, University of Caen, Caen, 14032, Cedex, France
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Kok E, van Dijk J, Voorhuijzen M, Staats M, Slot M, Lommen A, Venema D, Pla M, Corujo M, Barros E, Hutten R, Jansen J, van der Voet H. Omics analyses of potato plant materials using an improved one-class classification tool to identify aberrant compositional profiles in risk assessment procedures. Food Chem 2018; 292:350-358. [PMID: 31054687 DOI: 10.1016/j.foodchem.2018.07.224] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 07/24/2018] [Accepted: 07/31/2018] [Indexed: 10/28/2022]
Abstract
The objective of this study was to quantitatively assess potato omics profiles of new varieties for meaningful differences from analogous profiles of commercial varieties through the SIMCA one-class classification model. Analytical profiles of nine commercial potato varieties, eleven experimental potato varieties, one GM potato variety that had acquired Phytophtora resistance based on a single insert with potato-derived DNA sequences, and its non-GM commercial counterpart were generated. The ten conventional varieties were used to construct the one-class model. Omics profiles from experimental non-GM and GM varieties were assessed using the one-class SIMCA models. No potential unintended effects were identified in the case of the GM variety. The model showed that varieties that were genetically more distant from the commercial varieties were recognized as aberrant, highlighting its potential in determining whether additional evaluation is required for the risk assessment of materials produced from any breeding technique, including genetic modification.
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Affiliation(s)
- Esther Kok
- RIKILT Wageningen University & Research, Akkermaalsbos 2, 6708 WB Wageningen, the Netherlands.
| | - Jeroen van Dijk
- RIKILT Wageningen University & Research, Akkermaalsbos 2, 6708 WB Wageningen, the Netherlands
| | - Marleen Voorhuijzen
- RIKILT Wageningen University & Research, Akkermaalsbos 2, 6708 WB Wageningen, the Netherlands
| | - Martijn Staats
- RIKILT Wageningen University & Research, Akkermaalsbos 2, 6708 WB Wageningen, the Netherlands
| | - Martijn Slot
- RIKILT Wageningen University & Research, Akkermaalsbos 2, 6708 WB Wageningen, the Netherlands
| | - Arjen Lommen
- RIKILT Wageningen University & Research, Akkermaalsbos 2, 6708 WB Wageningen, the Netherlands
| | - Dini Venema
- RIKILT Wageningen University & Research, Akkermaalsbos 2, 6708 WB Wageningen, the Netherlands
| | - Maria Pla
- University of Girona, Institute for Food and Agricultural Technology (INTEA), Campus Montilivi (EPS-1), 17003 Girona, Spain
| | - Maria Corujo
- Centre for Research in Agricultural Genomics (CRAG), Edifici CRAG, Campus UAB, 08193 Cerdanyola, Barcelona, Spain
| | - Eugenia Barros
- Council for Scientific and Industrial Research (CSIR), Biosciences, Brummeria, Pretoria, South Africa
| | - Ronald Hutten
- Wageningen University & Research, Plant Breeding, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Jeroen Jansen
- University of Nijmegen, Comeniuslaan 4, 6525 HP Nijmegen, the Netherlands
| | - Hilko van der Voet
- Wageningen University & Research, Biometris, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
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Pinsorn P, Oikawa A, Watanabe M, Sasaki R, Ngamchuachit P, Hoefgen R, Saito K, Sirikantaramas S. Metabolic variation in the pulps of two durian cultivars: Unraveling the metabolites that contribute to the flavor. Food Chem 2018; 268:118-125. [PMID: 30064738 DOI: 10.1016/j.foodchem.2018.06.066] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 06/06/2018] [Accepted: 06/13/2018] [Indexed: 11/25/2022]
Abstract
Durian (Durio zibethinus M.) is a major economic fruit crop in Thailand. In this study, two popular cultivars, namely Chanee and Mon Thong, were collected from three orchards located in eastern Thailand. The pulp metabolome, including 157 annotated metabolites, was explored using capillary electrophoresis-time of flight/mass spectrometry (CE-TOF/MS). Cultivars and harvest years had more impact on metabolite profile separation than cultivation areas. We identified cultivar-dependent metabolite markers related to durian fruit quality traits, such as nutritional value (pyridoxamine), odor (cysteine, leucine), and ripening process (aminocyclopropane carboxylic acid). Interestingly, durian fruit were found to contain high amounts of γ-glutamylcysteine (810.3 ± 257.5 mg/100 g dry weight) and glutathione (158.1 ± 80.4 mg/100 g dry weight), which act as antioxidants and taste enhancers. This metabolite information could be related to consumer preferences and exploited for durian fruit quality improvement.
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Affiliation(s)
- Pinnapat Pinsorn
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand
| | - Akira Oikawa
- Faculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan; RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Mutsumi Watanabe
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany.
| | - Ryosuke Sasaki
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Panita Ngamchuachit
- Department of Food Technology, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand; Center of Molecular Sensory Science, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand.
| | - Rainer Hoefgen
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany.
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Supaart Sirikantaramas
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand; Omics Sciences and Bioinformatics Center, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand.
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Mazzei P, Cozzolino V, Piccolo A. High-Resolution Magic-Angle-Spinning NMR and Magnetic Resonance Imaging Spectroscopies Distinguish Metabolome and Structural Properties of Maize Seeds from Plants Treated with Different Fertilizers and Arbuscular mycorrhizal fungi. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:2580-2588. [PMID: 29323890 DOI: 10.1021/acs.jafc.7b04340] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Both high-resolution magic-angle-spinning (HRMAS) and magnetic resonance imaging (MRI) NMR spectroscopies were applied here to identify the changes of metabolome, morphology, and structural properties induced in seeds (caryopses) of maize plants grown at field level under either mineral or compost fertilization in combination with the inoculation by arbuscular mycorrhizal fungi (AMF). The metabolome of intact caryopses was examined by HRMAS-NMR, while the morphological aspects, endosperm properties and seed water distribution were investigated by MRI. Principal component analysis (PCA) was applied to evaluate 1H CPMG (Carr-Purcel-Meiboom-Gill) HRMAS spectra as well as several MRI-derived parameters ( T1, T2, and self-diffusion coefficients) of intact maize caryopses. PCA score-plots from spectral results indicated that both seeds metabolome and structural properties depended on the specific field treatment undergone by maize plants. Our findings show that a combination of multivariate statistical analyses with advanced and nondestructive NMR techniques, such as HRMAS and MRI, enables the evaluation of the effects induced on maize caryopses by different fertilization and management practices at field level. The spectroscopic approach adopted here may become useful for the objective appraisal of the quality of seeds produced under a sustainable agriculture.
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Yu X, Luo Q, Huang K, Yang G, He G. Prospecting for Microelement Function and Biosafety Assessment of Transgenic Cereal Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:326. [PMID: 29599791 PMCID: PMC5862831 DOI: 10.3389/fpls.2018.00326] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/27/2018] [Indexed: 05/26/2023]
Abstract
Microelement contents and metabolism are vitally important for cereal plant growth and development as well as end-use properties. While minerals phytotoxicity harms plants, microelement deficiency also affects human health. Genetic engineering provides a promising way to solve these problems. As plants vary in abilities to uptake, transport, and accumulate minerals, and the key enzymes acting on that process is primarily presented in this review. Subsequently, microelement function and biosafety assessment of transgenic cereal plants have become a key issue to be addressed. Progress in genetic engineering of cereal plants has been made with the introduction of quality, high-yield, and resistant genes since the first transgenic rice, corn, and wheat were born in 1988, 1990, and 1992, respectively. As the biosafety issue of transgenic cereal plants has now risen to be a top concern, many studies on transgenic biosafety have been carried out. Transgenic cereal biosafety issues mainly include two subjects, environmental friendliness and end-use safety. Different levels of gene confirmation, genomics, proteomics, metabolomics and nutritiomics, absorption, metabolism, and function have been investigated. Also, the different levels of microelement contents have been measured in transgenic plants. Based on the motivation of the requested biosafety, systematic designs, and analysis of transgenic cereal are also presented in this review paper.
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Affiliation(s)
- Xiaofen Yu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, China
| | - Qingchen Luo
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, China
| | - Kaixun Huang
- School of Chemistry and Chemical Engineering, Huazhong University of Science & Technology, Wuhan, China
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, China
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, China
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42
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Wang XJ, Zhang X, Yang JT, Wang ZX. Effect on transcriptome and metabolome of stacked transgenic maize containing insecticidal cry and glyphosate tolerance epsps genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:1007-1016. [PMID: 29356248 DOI: 10.1111/tpj.13825] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 12/13/2017] [Accepted: 12/21/2017] [Indexed: 05/18/2023]
Abstract
Gene stacking is a developing trend in agricultural biotechnology. Unintended effects in stacked transgenic plants are safety issues considered by the public and researchers. Omics techniques provide useful tools to assess unintended effects. In this paper, stacked transgenic maize 12-5×IE034 that contained insecticidal cry and glyphosate tolerance G10-epsps genes was obtained by crossing of transgenic maize varieties 12-5 and IE034. Transcriptome and metabolome analyses were performed for different maize varieties, including 12-5×IE034, 12-5, IE034, and conventional varieties collected from different provinces in China. The transcriptome results were as follows. The nine maize varieties had obvious differences in gene expression. There were 3561-5538 differentially expressed genes between 12-5×IE034 and its parents and transgenic receptor, which were far fewer than the number of differentially expressed genes in different traditional maize varieties. Cluster analysis indicated that there were close relationships between 12-5×IE034 and its parents. The metabolome results were as follows. For the nine detected maize varieties, the number of different metabolites ranged from 0 to 240. Compared with its parents, 12-5 and IE034, the hybrid variety 12-5×IE034 had 15 and 112 different metabolites, respectively. Hierarchical cluster analysis with Pearson's correlation analysis showed that the differences between 12-5×IE034 and its parents were fewer than those between other maize varieties. Shikimate pathway-related genes and metabolites analysis results showed that the effects of hybrid stacking are less than those from transformation and differing genotypes. Thus, the differences due to breeding stack were fewer than those due to natural variation among maize varieties. This paper provides scientific data for assessing unintended effects in stacked transgenic plants.
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Affiliation(s)
- Xu-Jing Wang
- Biotechnology Research Institute, Chinese Academy Agricultural Sciences, MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Beijing, 100081, China
| | - Xin Zhang
- Biotechnology Research Institute, Chinese Academy Agricultural Sciences, MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Beijing, 100081, China
| | - Jiang-Tao Yang
- Biotechnology Research Institute, Chinese Academy Agricultural Sciences, MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Beijing, 100081, China
| | - Zhi-Xing Wang
- Biotechnology Research Institute, Chinese Academy Agricultural Sciences, MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Beijing, 100081, China
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43
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Comparative analysis of miRNA expression profiles in transgenic and non-transgenic rice using miRNA-Seq. Sci Rep 2018; 8:338. [PMID: 29321648 PMCID: PMC5762784 DOI: 10.1038/s41598-017-18723-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 12/15/2017] [Indexed: 12/02/2022] Open
Abstract
Safety assessment for genetically modified organisms (GMOs) is required before their release. To date, miRNAs that play important roles in eukaryotic gene regulation have not been considered in the current assessment system. In this study, we identified 6 independent Bt and EPSPS GM rice lines using PCR and immune strip. We analyzed the expression levels of Cry1Ac and EPSPS using quantitative real-time PCR and western blot. Further, miRNAs from the developing seeds of the 6 GM rice lines and the wild-type line were investigated using deep sequencing and bioinformatic approaches. Although these GM lines have different types of integration sites, copy numbers, and levels of gene expression, 21 differentially expressed miRNAs have been found compared to wild type. There is no correlation between transgenic protein expression level and the quantity of differentially expressed miRNAs. This study provides useful data about the miRNA composition of GM plants, and it might be helpful for future risk assessments of miRNA-based GM plants.
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44
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Soares ALC, Geilfus CM, Carpentier SC. Genotype-Specific Growth and Proteomic Responses of Maize Toward Salt Stress. FRONTIERS IN PLANT SCIENCE 2018; 9:661. [PMID: 29899749 PMCID: PMC5989331 DOI: 10.3389/fpls.2018.00661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/30/2018] [Indexed: 05/20/2023]
Abstract
Salt stress in plants triggers complex physiological responses that are genotype specific. Many of these responses are either not yet described or not fully understood or both. In this work, we phenotyped three maize genotypes of the CIMMYT gene bank alongside the reference B73 genotype (NCRPIS - United States) under both control and salt-stressed conditions. We have ranked their growth potential and we observed significant differences in Na+ and Cl- ion accumulation. Genotype CML421 showed the slowest growth, while CML451 had the lowest accumulation of ions in its leaves. The phenotyping defined the right timing for the proteomics analysis, allowing us to compare the contrasting genotypes. In general 1,747 proteins were identified, of which 209 were significantly more abundant in response to salt stress. The five most significantly enriched annotations that positively correlated with stress were oxidation reduction, catabolic process, response to chemical stimulus, translational elongation and response to water. We observed a higher abundance of proteins involved in reactions to oxidative stress, dehydration, respiration, and translation. The five most significantly enriched annotations negatively correlated with stress were nucleosome organization, chromatin assembly, protein-DNA complex assembly, DNA packaging and nucleosome assembly. The genotypic analysis revealed 52 proteins that were correlated to the slow-growing genotype CML421. Their annotations point toward cellular dehydration and oxidative stress. Three root proteins correlated to the CML451 genotype were annotated to protein synthesis and ion compartmentalization. In conclusion, our results highlight the importance of the anti-oxidative system for acclimatization to salt stress and identify potential genotypic marker proteins involved in salt-stress responses.
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Affiliation(s)
- Ana L. C. Soares
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Leuven, Belgium
| | - Christoph-Martin Geilfus
- Controlled Environment Horticulture, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Sebastien C. Carpentier
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Leuven, Belgium
- Genetic Resources, Bioversity International, Leuven, Belgium
- SYBIOMA, KU Leuven, Leuven, Belgium
- *Correspondence: Sebastien C. Carpentier,
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McClain S, Stevenson SE, Brownie C, Herouet-Guicheney C, Herman RA, Ladics GS, Privalle L, Ward JM, Doerrer N, Thelen JJ. Variation in Seed Allergen Content From Three Varieties of Soybean Cultivated in Nine Different Locations in Iowa, Illinois, and Indiana. FRONTIERS IN PLANT SCIENCE 2018; 9:1025. [PMID: 30083174 PMCID: PMC6065051 DOI: 10.3389/fpls.2018.01025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 06/25/2018] [Indexed: 05/06/2023]
Abstract
Soybean (Glycine max) is an important food stock, and also considered an allergenic food with at least eight well characterized allergens. However, it is a less prevalent allergen source than many other foods and is rarely life-threatening. Soybean is incorporated into commonly consumed foods, and therefore, the allergens pose a potential concern for individuals already sensitized. The protein profile of soybean can be affected by several factors including genetic and environmental. To investigate how soybean allergen content may be affected by genetics and/or environment, nine soy allergens were quantified from three commercial soybean varieties grown at nine locations in three states within a single climate zone in North America; Iowa, Illinois, and Indiana, United States. Quantitation was achieved using liquid chromatography-selected reaction monitoring (LC-SRM) tandem mass spectrometry with AQUA peptide standards specific to the nine target allergens. Quantitation of allergen concentration indicated that both genetics and location affected specific allergen content. Seven of the nine allergens were significantly influenced by genetics, with the exceptions of glycinin G4 and KTI 3. The allergens P34, Gly m Bd 28k, glycinin G3, and KTI 1 showed statistically significant impact from location as well, but at a lower threshold of significance compared with genetics (cultivar/variety). This dataset contributes to our understanding of the natural variation of endogenous allergens, as it represents a sampling of soybeans grown in a controlled, distributed plot design under agronomic conditions common for commercial soybean food and feed production. The aim was to build upon our recent understanding of how allergens are expressed as part of the overall soybean proteome.
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Affiliation(s)
- Scott McClain
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, United States
- *Correspondence: Scott McClain,
| | - Severin E. Stevenson
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Cavell Brownie
- Department of Statistics, North Carolina State University, Raleigh, NC, United States
| | | | - Rod A. Herman
- Dow AgroSciences, Zionsville, Indianapolis, IN, United States
| | - Gregory S. Ladics
- Pioneer Hi-Bred, DuPont Agricultural Biotechnology, Wilmington, DE, United States
| | - Laura Privalle
- BASF Plant Science, Research Triangle Park, NC, United States
| | - Jason M. Ward
- Regulatory Affairs, Royal Canin, U.S.A., St. Charles, MO, United States
| | - Nancy Doerrer
- Protein Allergenicity Technical Committee, Health and Environmental Sciences Institute, Washington, DC, United States
| | - Jay J. Thelen
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
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Kumar R, Bohra A, Pandey AK, Pandey MK, Kumar A. Metabolomics for Plant Improvement: Status and Prospects. FRONTIERS IN PLANT SCIENCE 2017; 8:1302. [PMID: 28824660 PMCID: PMC5545584 DOI: 10.3389/fpls.2017.01302] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/11/2017] [Indexed: 05/12/2023]
Abstract
Post-genomics era has witnessed the development of cutting-edge technologies that have offered cost-efficient and high-throughput ways for molecular characterization of the function of a cell or organism. Large-scale metabolite profiling assays have allowed researchers to access the global data sets of metabolites and the corresponding metabolic pathways in an unprecedented way. Recent efforts in metabolomics have been directed to improve the quality along with a major focus on yield related traits. Importantly, an integration of metabolomics with other approaches such as quantitative genetics, transcriptomics and genetic modification has established its immense relevance to plant improvement. An effective combination of these modern approaches guides researchers to pinpoint the functional gene(s) and the characterization of massive metabolites, in order to prioritize the candidate genes for downstream analyses and ultimately, offering trait specific markers to improve commercially important traits. This in turn will improve the ability of a plant breeder by allowing him to make more informed decisions. Given this, the present review captures the significant leads gained in the past decade in the field of plant metabolomics accompanied by a brief discussion on the current contribution and the future scope of metabolomics to accelerate plant improvement.
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Affiliation(s)
- Rakesh Kumar
- Department of Plant Sciences, University of Hyderabad (UoH)Hyderabad, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Abhishek Bohra
- Crop Improvement Division, Indian Institute of Pulses Research (IIPR)Kanpur, India
| | - Arun K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University (IGNTU)Amarkantak, India
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Ndimba RJ, Kruger J, Mehlo L, Barnabas A, Kossmann J, Ndimba BK. A Comparative Study of Selected Physical and Biochemical Traits of Wild-Type and Transgenic Sorghum to Reveal Differences Relevant to Grain Quality. FRONTIERS IN PLANT SCIENCE 2017; 8:952. [PMID: 28638394 PMCID: PMC5461292 DOI: 10.3389/fpls.2017.00952] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 05/22/2017] [Indexed: 06/14/2023]
Abstract
Transgenic sorghum featuring RNAi suppression of certain kafirins was developed recently, to address the problem of poor protein digestibility in the grain. However, it was not firmly established if other important quality parameters were adversely affected by this genetic intervention. In the present study several quality parameters were investigated by surveying several important physical and biochemical grain traits. Important differences in grain weight, density and endosperm texture were found that serve to differentiate the transgenic grains from their wild-type counterpart. In addition, ultrastructural analysis of the protein bodies revealed a changed morphology that is indicative of the effect of suppressed kafirins. Importantly, lysine was found to be significantly increased in one of the transgenic lines in comparison to wild-type; while no significant changes in anti-nutritional factors could be detected. The results have been insightful for demonstrating some of the corollary changes in transgenic sorghum grain, that emerge from imposed kafirin suppression.
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Affiliation(s)
- Roya J. Ndimba
- iThemba LABS, National Research FoundationCape Town, South Africa
- Institute for Plant Biotechnology, University of StellenboschMatieland, South Africa
| | - Johanita Kruger
- Department of Food Science and Institute for Food Nutrition and Well-Being, University of PretoriaPretoria, South Africa
| | - Luke Mehlo
- Enterprise Creation for Development Unit, Council for Scientific and Industrial ResearchPretoria, South Africa
| | - Alban Barnabas
- iThemba LABS, National Research FoundationCape Town, South Africa
| | - Jens Kossmann
- Institute for Plant Biotechnology, University of StellenboschMatieland, South Africa
| | - Bongani K. Ndimba
- Agricultural Research Council, Infruitec-NietvoorbijStellenbosch, South Africa
- Proteomics Unit, Department of Biotechnology, University of the Western CapeBellville, South Africa
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Molecular responses of genetically modified maize to abiotic stresses as determined through proteomic and metabolomic analyses. PLoS One 2017; 12:e0173069. [PMID: 28245233 PMCID: PMC5330488 DOI: 10.1371/journal.pone.0173069] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/14/2017] [Indexed: 01/08/2023] Open
Abstract
Some genetically modified (GM) plants have transgenes that confer tolerance to abiotic stressors. Meanwhile, other transgenes may interact with abiotic stressors, causing pleiotropic effects that will affect the plant physiology. Thus, physiological alteration might have an impact on the product safety. However, routine risk assessment (RA) analyses do not evaluate the response of GM plants exposed to different environmental conditions. Therefore, we here present a proteome profile of herbicide-tolerant maize, including the levels of phytohormones and related compounds, compared to its near-isogenic non-GM variety under drought and herbicide stresses. Twenty differentially abundant proteins were detected between GM and non-GM hybrids under different water deficiency conditions and herbicide sprays. Pathway enrichment analysis showed that most of these proteins are assigned to energetic/carbohydrate metabolic processes. Among phytohormones and related compounds, different levels of ABA, CA, JA, MeJA and SA were detected in the maize varieties and stress conditions analysed. In pathway and proteome analyses, environment was found to be the major source of variation followed by the genetic transformation factor. Nonetheless, differences were detected in the levels of JA, MeJA and CA and in the abundance of 11 proteins when comparing the GM plant and its non-GM near-isogenic variety under the same environmental conditions. Thus, these findings do support molecular studies in GM plants Risk Assessment analyses.
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Hradilová I, Trněný O, Válková M, Cechová M, Janská A, Prokešová L, Aamir K, Krezdorn N, Rotter B, Winter P, Varshney RK, Soukup A, Bednář P, Hanáček P, Smýkal P. A Combined Comparative Transcriptomic, Metabolomic, and Anatomical Analyses of Two Key Domestication Traits: Pod Dehiscence and Seed Dormancy in Pea ( Pisum sp.). FRONTIERS IN PLANT SCIENCE 2017; 8:542. [PMID: 28487704 PMCID: PMC5404241 DOI: 10.3389/fpls.2017.00542] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/27/2017] [Indexed: 05/19/2023]
Abstract
The origin of the agriculture was one of the turning points in human history, and a central part of this was the evolution of new plant forms, domesticated crops. Seed dispersal and germination are two key traits which have been selected to facilitate cultivation and harvesting of crops. The objective of this study was to analyze anatomical structure of seed coat and pod, identify metabolic compounds associated with water-impermeable seed coat and differentially expressed genes involved in pea seed dormancy and pod dehiscence. Comparative anatomical, metabolomics, and transcriptomic analyses were carried out on wild dormant, dehiscent Pisum elatius (JI64, VIR320) and cultivated, indehiscent Pisum sativum non-dormant (JI92, Cameor) and recombinant inbred lines (RILs). Considerable differences were found in texture of testa surface, length of macrosclereids, and seed coat thickness. Histochemical and biochemical analyses indicated genotype related variation in composition and heterogeneity of seed coat cell walls within macrosclereids. Liquid chromatography-electrospray ionization/mass spectrometry and Laser desorption/ionization-mass spectrometry of separated seed coats revealed significantly higher contents of proanthocyanidins (dimer and trimer of gallocatechin), quercetin, and myricetin rhamnosides and hydroxylated fatty acids in dormant compared to non-dormant genotypes. Bulk Segregant Analysis coupled to high throughput RNA sequencing resulted in identification of 770 and 148 differentially expressed genes between dormant and non-dormant seeds or dehiscent and indehiscent pods, respectively. The expression of 14 selected dormancy-related genes was studied by qRT-PCR. Of these, expression pattern of four genes: porin (MACE-S082), peroxisomal membrane PEX14-like protein (MACE-S108), 4-coumarate CoA ligase (MACE-S131), and UDP-glucosyl transferase (MACE-S139) was in agreement in all four genotypes with Massive analysis of cDNA Ends (MACE) data. In case of pod dehiscence, the analysis of two candidate genes (SHATTERING and SHATTERPROOF) and three out of 20 MACE identified genes (MACE-P004, MACE-P013, MACE-P015) showed down-expression in dorsal and ventral pod suture of indehiscent genotypes. Moreover, MACE-P015, the homolog of peptidoglycan-binding domain or proline-rich extensin-like protein mapped correctly to predicted Dpo1 locus on PsLGIII. This integrated analysis of the seed coat in wild and cultivated pea provides new insight as well as raises new questions associated with domestication and seed dormancy and pod dehiscence.
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Affiliation(s)
- Iveta Hradilová
- Department of Botany, Palacký University in OlomoucOlomouc, Czechia
| | - Oldřich Trněný
- Department of Plant Biology, Mendel University in BrnoBrno, Czechia
- Agricultural Research, Ltd.Troubsko, Czechia
| | - Markéta Válková
- Department of Analytical Chemistry, Regional Centre of Advanced Technologies and Materials, Palacký University in OlomoucOlomouc, Czechia
- Faculty of Science, Palacký University in OlomoucOlomouc, Czechia
| | - Monika Cechová
- Department of Analytical Chemistry, Regional Centre of Advanced Technologies and Materials, Palacký University in OlomoucOlomouc, Czechia
- Faculty of Science, Palacký University in OlomoucOlomouc, Czechia
| | - Anna Janská
- Department of Experimental Plant Biology, Charles UniversityPrague, Czechia
| | - Lenka Prokešová
- Department of Crop Science, Breeding and Plant Medicine, Mendel University in BrnoBrno, Czechia
| | - Khan Aamir
- Research Program-Genetic Gains, ICRISATHyderabad, India
| | | | | | | | | | - Aleš Soukup
- Department of Experimental Plant Biology, Charles UniversityPrague, Czechia
| | - Petr Bednář
- Department of Analytical Chemistry, Regional Centre of Advanced Technologies and Materials, Palacký University in OlomoucOlomouc, Czechia
- Faculty of Science, Palacký University in OlomoucOlomouc, Czechia
| | - Pavel Hanáček
- Department of Plant Biology, Mendel University in BrnoBrno, Czechia
| | - Petr Smýkal
- Department of Botany, Palacký University in OlomoucOlomouc, Czechia
- *Correspondence: Petr Smýkal
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50
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Mesnage R, Agapito-Tenfen SZ, Vilperte V, Renney G, Ward M, Séralini GE, Nodari RO, Antoniou MN. An integrated multi-omics analysis of the NK603 Roundup-tolerant GM maize reveals metabolism disturbances caused by the transformation process. Sci Rep 2016; 6:37855. [PMID: 27991589 PMCID: PMC5171704 DOI: 10.1038/srep37855] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/02/2016] [Indexed: 12/22/2022] Open
Abstract
Glyphosate tolerant genetically modified (GM) maize NK603 was assessed as 'substantially equivalent' to its isogenic counterpart by a nutrient composition analysis in order to be granted market approval. We have applied contemporary in depth molecular profiling methods of NK603 maize kernels (sprayed or unsprayed with Roundup) and the isogenic corn to reassess its substantial equivalence status. Proteome profiles of the maize kernels revealed alterations in the levels of enzymes of glycolysis and TCA cycle pathways, which were reflective of an imbalance in energy metabolism. Changes in proteins and metabolites of glutathione metabolism were indicative of increased oxidative stress. The most pronounced metabolome differences between NK603 and its isogenic counterpart consisted of an increase in polyamines including N-acetyl-cadaverine (2.9-fold), N-acetylputrescine (1.8-fold), putrescine (2.7-fold) and cadaverine (28-fold), which depending on context can be either protective or a cause of toxicity. Our molecular profiling results show that NK603 and its isogenic control are not substantially equivalent.
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Affiliation(s)
- Robin Mesnage
- Gene Expression and Therapy Group, King’s College London, Faculty of Life Sciences & Medicine, Department of Medical and Molecular Genetics, 8th Floor, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | | | - Vinicius Vilperte
- CropScience Department, Federal University of Santa Catarina, Rod. Admar Gonzaga 1346, 88034-000 Florianópolis, Brazil
| | - George Renney
- Proteomics Facility, King’s College London, Institute of Psychiatry, London SE5 8AF, United Kingdom
| | - Malcolm Ward
- Proteomics Facility, King’s College London, Institute of Psychiatry, London SE5 8AF, United Kingdom
| | - Gilles-Eric Séralini
- University of Caen, Institute of Biology, EA 2608 and Network on Risks, Quality and Sustainable Environment, MRSH, Esplanade de la Paix, University of Caen, Caen 14032, Cedex, France
| | - Rubens O. Nodari
- CropScience Department, Federal University of Santa Catarina, Rod. Admar Gonzaga 1346, 88034-000 Florianópolis, Brazil
| | - Michael N. Antoniou
- Gene Expression and Therapy Group, King’s College London, Faculty of Life Sciences & Medicine, Department of Medical and Molecular Genetics, 8th Floor, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
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